You can subscribe to this list here.
2008 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(2) |
Sep
|
Oct
(1) |
Nov
(3) |
Dec
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
2009 |
Jan
(2) |
Feb
|
Mar
(1) |
Apr
(1) |
May
(1) |
Jun
|
Jul
(1) |
Aug
(4) |
Sep
|
Oct
(2) |
Nov
(2) |
Dec
(1) |
2010 |
Jan
(1) |
Feb
|
Mar
(4) |
Apr
(2) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
(1) |
2011 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(1) |
Jun
(2) |
Jul
(5) |
Aug
|
Sep
|
Oct
|
Nov
(4) |
Dec
(2) |
2012 |
Jan
|
Feb
(2) |
Mar
|
Apr
(2) |
May
|
Jun
(3) |
Jul
(1) |
Aug
(9) |
Sep
(4) |
Oct
|
Nov
(1) |
Dec
|
2013 |
Jan
|
Feb
(5) |
Mar
|
Apr
(6) |
May
|
Jun
(2) |
Jul
|
Aug
(2) |
Sep
(3) |
Oct
|
Nov
|
Dec
(3) |
2014 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(1) |
Jun
|
Jul
(2) |
Aug
(1) |
Sep
|
Oct
|
Nov
(2) |
Dec
(15) |
2015 |
Jan
(7) |
Feb
(7) |
Mar
(12) |
Apr
(3) |
May
(4) |
Jun
(6) |
Jul
|
Aug
|
Sep
(9) |
Oct
(1) |
Nov
(3) |
Dec
(8) |
2016 |
Jan
(3) |
Feb
(4) |
Mar
(7) |
Apr
(6) |
May
(7) |
Jun
|
Jul
(3) |
Aug
(4) |
Sep
(1) |
Oct
(13) |
Nov
(4) |
Dec
(4) |
2017 |
Jan
(6) |
Feb
(8) |
Mar
(6) |
Apr
|
May
(3) |
Jun
(1) |
Jul
(6) |
Aug
|
Sep
|
Oct
|
Nov
(5) |
Dec
(2) |
2018 |
Jan
(3) |
Feb
(2) |
Mar
|
Apr
(2) |
May
|
Jun
(2) |
Jul
(2) |
Aug
|
Sep
|
Oct
(3) |
Nov
(3) |
Dec
|
2019 |
Jan
(2) |
Feb
(7) |
Mar
|
Apr
|
May
(11) |
Jun
(9) |
Jul
|
Aug
(2) |
Sep
(4) |
Oct
|
Nov
(3) |
Dec
|
2020 |
Jan
(12) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
2022 |
Jan
|
Feb
|
Mar
|
Apr
(2) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
(9) |
Dec
(2) |
2023 |
Jan
|
Feb
(2) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
|
From: Maria L. <chi...@cs...> - 2023-08-15 12:58:16
|
Hi Martina! It is a bit difficult to get the full picture of your experimental design, but setting the control samples as the intercept sounds correct. We can take a closer look at your experimental setup and design, if you wish. For that, you would need to send us a support request via Chipster and share your session (in Chipster: contact -> contact support -> attach session). This gives us (=the Chipster team) a permission to look at a snapshot of your session. Chapter 3.2.5 in the edgeR manual explains the intercept: http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf Maybe the key point is here: “-- the first coefficient will measure the baseline logCPM expression level in the first treatment condition (here group A), and the second and third columns are relative to the baseline. - - This parametrization makes good sense when the first group represents a reference or control group, as all comparison are made with respect to this condition. Note that > qlf <- glmQLFTest(fit2, coef=1) [the first coefficient = the intercept] should not be used. It would test whether the first coefficient is zero, but it is not meaningful to compare the logCPM in group A to zero.” So the intercept (= group A or in your case the control group) is the baseline expression level. It is not normalised to 1. All the other groups are compared to this baseline level. Looking at the intercept column is like looking at the comparison of group A (= control group) to zero, which is not meaningful, as we expect some level of expression in this group as well. First meaningful comparison is the second one, comparing group A to group B ( B-A, in your case condition1 - control). Positive fold-change here would mean that expression in group B is higher than in group A. Regarding the analysis steps, we have training material for the RNAseq workflow steps here: https://chipster.rahtiapp.fi/manual/courses.html#rna In our trainings and training material, we aim at explaining the steps first in an intuitive level, allowing the users to then dig deeper into the statistics when & where needed. Hope this helps! Maria L / Chipster team > On 14. Aug 2023, at 11.43, Lorey, Martina B <mar...@he...> wrote: > > Hi, sorry this is probably a silly question but here it goes: I have quite a few conditions and wanted to compare them all, including the controls, in a first step to the untreated cells (also to see if the controls induce any funny things). So, I compiled and ngs experiment and ran it through edgeR, with untreated as the intercept. What confuses me profoundly is that I assumed the log FC of the intercept would be normalised to 1 and all others go up and down in comparison with that, but the logFCs for the intercept are all over. Did I do something wrong or do I misunderstand something crucial? What would be the next step to normalise, or should that have been done before? I am helpful for any advice to the the not-really-statistic-literate. > > BR Martina > > > > ---------------------------------------------------------------------------- > Martina Lorey, PhD > Atherosclerosis Research Laboratory, Wihuri Research Institute > Biomedicum Helsinki > Haartmaninkatu 8 > FI-00290 HELSINKI > Finland > _______________________________________________ > Chipster-users mailing list > Chi...@li... <mailto:Chi...@li...> > https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Lorey, M. B <mar...@he...> - 2023-08-14 10:16:15
|
Hi, sorry this is probably a silly question but here it goes: I have quite a few conditions and wanted to compare them all, including the controls, in a first step to the untreated cells (also to see if the controls induce any funny things). So, I compiled and ngs experiment and ran it through edgeR, with untreated as the intercept. What confuses me profoundly is that I assumed the log FC of the intercept would be normalised to 1 and all others go up and down in comparison with that, but the logFCs for the intercept are all over. Did I do something wrong or do I misunderstand something crucial? What would be the next step to normalise, or should that have been done before? I am helpful for any advice to the the not-really-statistic-literate. BR Martina ---------------------------------------------------------------------------- Martina Lorey, PhD Atherosclerosis Research Laboratory, Wihuri Research Institute Biomedicum Helsinki Haartmaninkatu 8 FI-00290 HELSINKI Finland |
From: <chi...@cs...> - 2023-02-02 09:04:15
|
Hi Zilan, Thank you for proposing these genomes. What kind of analysis would you like to do with them (I'm asking this, because each aligner has its own index structure)? In general we use genomes from the Ensembl database and we have an automated system to retrieve and index them. For genomes that are not in Ensembl, we typically advice the user to perform the indexing in Chipster and then use these "private" indexes in the subsequent alignment jobs. However, in your case that would be possible only for the two pathogen genomes, because the tree genomes are too big. If it turns out that this is not possible to do in Chipster, we can guide you on how to use CSC's supercomputers coupled to storage systems. Best, Eija From: "zilan wen" <zil...@he...> To: "chipster-users" <chi...@li...> Sent: Wednesday, 1 February, 2023 14:19:47 Subject: [Chipster-users] Add new reference genome Hi Chipster, Is it possible to add reference genomes of Picea abies (19.6 G), Pinus taeda (20.6 G), Heterobasidion parviporum (37.76MB), Heterobasidion annosum (Fr.) Bref. sensu stricto (s.s.) (31.01MB) into Chipter. For example Pinus taeda genome: https://plantgenie.org/FTP?dir=Data%2FPlantGenIE%2FPinus_taeda%2Fv2.01 The draft genome sequence of Heterobasidion annosum s.s. can be found at DDBJ/EMBL/GenBank under accession no. AOSL00000000. The Whole Genome Shotgun project of the H. parviporum 96026 has been deposited at DDBJ/ ENA/GenBank (https://www.ncbi.nlm.nih.gov/genome/) under the accession PDUQ00000000. I have files related to H. parviporum reference genome. [ https://plantgenie.org/FTP?dir=Data%2FPlantGenIE%2FPinus_taeda%2Fv2.01 ] Best regards, Zilan Wen ----------------------------------- Zilan Wen PhD Department of Forest Sciences P.O.Box 27 (Latokartanonkaari 7) FI-00014, room K116. University of Helsinki, Finland Phone: +358 401681092 _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Wen, Z. <zil...@he...> - 2023-02-01 12:35:51
|
Hi Chipster, Is it possible to add reference genomes of Picea abies (19.6 G), Pinus taeda (20.6 G), Heterobasidion parviporum (37.76MB), Heterobasidion annosum (Fr.) Bref. sensu stricto (s.s.) (31.01MB) into Chipter. For example Pinus taeda genome: https://plantgenie.org/FTP?dir=Data%2FPlantGenIE%2FPinus_taeda%2Fv2.01 The draft genome sequence of Heterobasidion annosum s.s. can be found at DDBJ/EMBL/GenBank under accession no. AOSL00000000. The Whole Genome Shotgun project of the H. parviporum 96026 has been deposited at DDBJ/ ENA/GenBank (https://www.ncbi.nlm.nih.gov/genome/) under the accession PDUQ00000000. I have files related to H. parviporum reference genome. <https://plantgenie.org/FTP?dir=Data%2FPlantGenIE%2FPinus_taeda%2Fv2.01> Best regards, Zilan Wen ----------------------------------- Zilan Wen PhD Department of Forest Sciences P.O.Box 27 (Latokartanonkaari 7) FI-00014, room K116. University of Helsinki, Finland Phone: +358 401681092 |
From: <chi...@cs...> - 2022-12-02 11:37:51
|
Thanks a lot Oliver, I just merged it to our Master branch. Have a nice weekend, Eija From: "Oliver Heil" <o....@dk...> To: "chipster-users" <chi...@li...> Sent: Thursday, 1 December, 2022 13:29:24 Subject: Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Hi Eija, The PR for the split tool is set. [ https://github.com/chipster/chipster-tools/pull/18 | https://github.com/chipster/chipster-tools/pull/18 ] Regards, Oli Am 30.11.2022 um 14:01 schrieb [ mailto:chi...@cs... | chi...@cs... ] : Hi Oli, Ok, thank you for clarifying and good that lumi works on your server too, I was already worried. The container architecture has been working fine for us, but I totally understand your frustration. I wonder if we should schedule a technical meeting in Zoom to understand better what is the difference in your setup so that we can troubleshoot better? Anyhow, good that your server works again. Please make a pull request when you have tested the splitting tool, thank you so much for making it! Best, Eija -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Oliver H. <o....@dk...> - 2022-12-01 11:29:39
|
Hi Eija, The PR for the split tool is set. https://github.com/chipster/chipster-tools/pull/18 Regards, Oli Am 30.11.2022 um 14:01 schrieb chi...@cs...: > Hi Oli, > > Ok, thank you for clarifying and good that lumi works on your server > too, I was already worried. > > The container architecture has been working fine for us, but I totally > understand your frustration. I wonder if we should schedule a > technical meeting in Zoom to understand better what is the difference > in your setup so that we can troubleshoot better? Anyhow, good that > your server works again. > > Please make a pull request when you have tested the splitting tool, > thank you so much for making it! > > Best, > Eija > > ------------------------------------------------------------------------ > -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
From: <chi...@cs...> - 2022-11-30 13:01:30
|
Hi Oli, Ok, thank you for clarifying and good that lumi works on your server too, I was already worried. The container architecture has been working fine for us, but I totally understand your frustration. I wonder if we should schedule a technical meeting in Zoom to understand better what is the difference in your setup so that we can troubleshoot better? Anyhow, good that your server works again. Please make a pull request when you have tested the splitting tool, thank you so much for making it! Best, Eija From: "Oliver Heil" <o....@dk...> To: "chipster-users" <chi...@li...> Sent: Tuesday, 29 November, 2022 16:28:16 Subject: Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Hi Eija, no, no, I think we are on a side track here. The problem is not about lumi. You brought lumi up as a tool for data imported as a whole table. For this to work, the table needs to be in a specific format as described in lumis documentation. I just said, that I tried with lumi (for our specific data table, which is not in the right format) and I got an error. That's totally fine. It should not work with our specific data table. We can bring it into the right format, to have a workaround. Lumi is fine! A more general way to use tables is having a split tool. That's where I am still on. And all this around, distracting from the real problem I try to solve, are those issues with containers, chipster not restarting, and so on. Actually, my opinion is, the whole container architecture is a mess. Not only the specific chipster architecture, but containers in general. Well, I have to admit, I am still not an expert when it comes to containers/docker/...whatever, my motivation to become an expert on containers is literally zero. So, let me role us all back in time: I just want to have the documentation of my new split tool visible in our chipster installation (other thread with Petri), but I am failing miserably. There is no current issue with lumi. Best, Oli Am 29.11.2022 um 14:57 schrieb [ mailto:chi...@cs... | chi...@cs... ] : Hi Oliver, Sorry to hear that running the tool "Illumina - lumi pipeline" brought Chipster in to a bad state! I just tested lumi on our server and it produced normalized data and phenodata without any error message. While our technical guys can hopefully help you to sort out the server situation, I would like to ask more about the actual lumi job you were trying to run. You wrote that the imported file does not comply to the needed format like column names. I'm puzzled by this, because when you click the green "Add file" button it brings the file in exactly as it is. For the lumi pipeline the input file is the BeadStudio / GenomeStudio output file, so no conversion is needed. I tested with a file from BeadStudio version 1.5.0.34, but if you send me a newer file I can test with that too. Best, Eija-- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Chipster <chi...@cs...> - 2022-11-29 14:42:12
|
Hi, well, that certainly is unexpected. I can't even imagine how the tool could bring down all other Chipster services, unless the whole machine runs out of memory. The tool shouldn't be able to use more than 8 GB of ram, and I assume that you have more than 16 GB, so that shouldn't be an issue. Is there any clues why the pods are in error state if you check the pod events with: kubectl describe pod POD_NAME You can copy the pod name from the "kubectl get pod". The pods comp-job... and scheduler are the most interesting. If that doesn't show anything, maybe then logs: kubectl logs POD_NAME | tail -n 30 Best regards, Petri > On 29. Nov 2022, at 14.55, Oliver Heil <o....@dk...> wrote: > > Hi Eija, > > >> If you have a chance to test Lumi again and get an error, please let me know what the error message is. > > the imported file does not comply to the needed format like column names. > So the error is not unexpected. > > I wanted to show the error anyways (i remember it was rather short) so started a lumi job. > This brought chipster now into a bad state: > > <y2nH17ENnZM0v200.png> > > > > There it is for quite some time now. > > This is all together not very smooth and expedient but I can't help. > I am waiting now until this chipster installation regenerates again. > > Regards, > > Oli > > Am 25.11.2022 um 13:20 schrieb chi...@cs... <mailto:chi...@cs...>: >> Hi Oliver, >> >> Thank you for creating the splitting tool. When it is ready and you have tested it in the DKFZ installation, please make a pull request. PR in GitHub is indeed the way to go and I have seen the previous ones (and accepted one of them). I will accept the PR for the splitting tool as soon as it comes. Thanks a lot already in advance! >> >> If you have a chance to test Lumi again and get an error, please let me know what the error message is. >> >> Best, >> Eija >> >> From: "Oliver Heil" <o....@dk...> <mailto:o....@dk...> >> To: "chipster-users" <chi...@li...> <mailto:chi...@li...> >> Sent: Friday, 25 November, 2022 10:33:14 >> Subject: Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) >> >> Hi Eija, >> >> yes, I already experimented with Lumi but I got another error (which >> I can't remember for now), but in general I think it is needed for the >> other Norm->Illumina tools. >> >> Currently I have created a split tool by taking the join tool as a template >> and it works fine so far. It's still a bit experimental and doc is not yet >> visible in our chipster installation, but Petri did a great job supporting >> me with tips. I will finish everything next week. >> >> Actually I would do a PR in github but my older PRs are waiting since I made them >> last year (?) without any discussion, so I am not sure if this the way to >> provide some contributions. >> (https://github.com/chipster/chipster-tools/pulls <https://github.com/chipster/chipster-tools/pulls>) >> >> Regards, >> >> Oli >> >> Am 25.11.2022 um 08:43 schrieb chi...@cs... <mailto:chi...@cs...>: >> Hi Oliver, >> >> You are right, the former Import tool was replaced in the web based Chipster by the "Convert to Chipster format" option, which allows the user to mark id, sample and other columns, but it doesn't do splitting (people typically use it for RNA-seq count tables). Our Illumina array users use the lumi pipeline which takes a whole file, so it hasn't been a problem. However, if there are users who prefer to use the older Illumina normalization tool, we need to look into this. >> >> Making a separate splitting tool like you mentioned might be a better option than modifying the "Convert to Chipster format" functionality, because the latter produces also phenodata and is thus more geared for normalized data. If you want to check out how this system works, select a tsv file, click the three dots after the filename in the File panel and select "Convert to Chipster format". Please let me know what you think and thank you for bringing the problem to our attention! >> >> Best, >> Eija >> >> From: "Oliver Heil" <o....@dk...> <mailto:o....@dk...> >> To: "chipster-users" <chi...@li...> <mailto:chi...@li...> >> Sent: Wednesday, 23 November, 2022 11:54:37 >> Subject: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) >> >> Dear Chipster people, >> >> In earlier versions we had the option to import table like data into >> Chipster via the Import Tool. During which each sample column was >> created as separate file in Chipster. Tools like "Normalisation" -> "Illumina" >> expect this type of raw data. >> >> With v4 this seems to be a problem now. I can't find anything like the >> old Import Tool which produces separate Chipster files for each e.g. column >> in a tab separated .tsv file. In "Misc" -> "Utilitities" there is a "Join tables" but >> we need a "Split table", isn't it? >> >> Any idea how to process old microarray expression data, which is a >> tab separated file with columns like >> ProbeID sample1 sample2 sample3 ... >> ? >> >> Regards, >> >> Oli >> >> -- >> Oliver Heil >> Microarray Core Facility >> Bioinformatics >> >> German Cancer Research Center (DKFZ) >> Foundation under Public Law >> Im Neuenheimer Feld 580 >> 69120 Heidelberg >> Germany >> >> o....@dk... <mailto:o....@dk...> >> Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> >> www.dkfz.de <http://www.dkfz.de/> >> <9ZymfqecUHxRKI0V.jpg> >> Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich >> VAT-ID No.: DE143293537 >> >> >> >> _______________________________________________ >> Chipster-users mailing list >> Chi...@li... <mailto:Chi...@li...> >> https://lists.sourceforge.net/lists/listinfo/chipster-users <https://lists.sourceforge.net/lists/listinfo/chipster-users> >> >> >> >> >> _______________________________________________ >> Chipster-users mailing list >> Chi...@li... <mailto:Chi...@li...> >> https://lists.sourceforge.net/lists/listinfo/chipster-users <https://lists.sourceforge.net/lists/listinfo/chipster-users> >> >> >> _______________________________________________ >> Chipster-users mailing list >> Chi...@li... <mailto:Chi...@li...> >> https://lists.sourceforge.net/lists/listinfo/chipster-users <https://lists.sourceforge.net/lists/listinfo/chipster-users> >> >> >> >> >> _______________________________________________ >> Chipster-users mailing list >> Chi...@li... <mailto:Chi...@li...> >> https://lists.sourceforge.net/lists/listinfo/chipster-users <https://lists.sourceforge.net/lists/listinfo/chipster-users> > -- > Oliver Heil > Microarray Core Facility > Bioinformatics > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > > o....@dk... <mailto:o....@dk...> > Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> > www.dkfz.de <http://www.dkfz.de/><g0H1JBgwi0SrPE0Y.jpg> > Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > > _______________________________________________ > Chipster-users mailing list > Chi...@li... <mailto:Chi...@li...> > https://lists.sourceforge.net/lists/listinfo/chipster-users <https://lists.sourceforge.net/lists/listinfo/chipster-users> |
From: Oliver H. <o....@dk...> - 2022-11-29 14:28:26
|
Hi Eija, no, no, I think we are on a side track here. The problem is not about lumi. You brought lumi up as a tool for data imported as a whole table. For this to work, the table needs to be in a specific format as described in lumis documentation. I just said, that I tried with lumi (for our specific data table, which is not in the right format) and I got an error. That's totally fine. It should not work with our specific data table. We can bring it into the right format, to have a workaround. Lumi is fine! A more general way to use tables is having a split tool. That's where I am still on. And all this around, distracting from the real problem I try to solve, are those issues with containers, chipster not restarting, and so on. Actually, my opinion is, the whole container architecture is a mess. Not only the specific chipster architecture, but containers in general. Well, I have to admit, I am still not an expert when it comes to containers/docker/...whatever, my motivation to become an expert on containers is literally zero. So, let me role us all back in time: I just want to have the documentation of my new split tool visible in our chipster installation (other thread with Petri), but I am failing miserably. There is no current issue with lumi. Best, Oli Am 29.11.2022 um 14:57 schrieb chi...@cs...: > Hi Oliver, > > Sorry to hear that running the tool "Illumina - lumi pipeline" brought > Chipster in to a bad state! I just tested lumi on our server and it > produced normalized data and phenodata without any error message. > While our technical guys can hopefully help you to sort out the server > situation, I would like to ask more about the actual lumi job you were > trying to run. > > You wrote that the imported file does not comply to the needed format > like column names. I'm puzzled by this, because when you click the > green "Add file" button it brings the file in exactly as it is. For > the lumi pipeline the input file is the BeadStudio / GenomeStudio > output file, so no conversion is needed. I tested with a file from > BeadStudio version 1.5.0.34, but if you send me a newer file I can > test with that too. > > Best, > Eija-- > > Oliver Heil > Microarray Core Facility > Bioinformatics > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > > o....@dk... <mailto:o....@dk...> > Support: www.dkfz.de/gpcf/phpBB3/index.php > <https://www.dkfz.de/gpcf/phpBB3/index.php> > www.dkfz.de <http://www.dkfz.de> > > Research for a Life without Cancer > > Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > |
From: <chi...@cs...> - 2022-11-29 13:57:46
|
Hi Oliver, Sorry to hear that running the tool "Illumina - lumi pipeline" brought Chipster in to a bad state! I just tested lumi on our server and it produced normalized data and phenodata without any error message. While our technical guys can hopefully help you to sort out the server situation, I would like to ask more about the actual lumi job you were trying to run. You wrote that the imported file does not comply to the needed format like column names. I'm puzzled by this, because when you click the green "Add file" button it brings the file in exactly as it is. For the lumi pipeline the input file is the BeadStudio / GenomeStudio output file, so no conversion is needed. I tested with a file from BeadStudio version 1.5.0.34, but if you send me a newer file I can test with that too. Best, Eija From: "Oliver Heil" <o....@dk...> To: "chipster-users" <chi...@li...> Sent: Tuesday, 29 November, 2022 14:55:25 Subject: Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Hi Eija, If you have a chance to test Lumi again and get an error, please let me know what the error message is. the imported file does not comply to the needed format like column names. So the error is not unexpected. I wanted to show the error anyways (i remember it was rather short) so started a lumi job. This brought chipster now into a bad state: There it is for quite some time now. This is all together not very smooth and expedient but I can't help. I am waiting now until this chipster installation regenerates again. Regards, Oli Am 25.11.2022 um 13:20 schrieb [ mailto:chi...@cs... | chi...@cs... ] : BQ_BEGIN Hi Oliver, Thank you for creating the splitting tool. When it is ready and you have tested it in the DKFZ installation, please make a pull request. PR in GitHub is indeed the way to go and I have seen the previous ones (and accepted one of them). I will accept the PR for the splitting tool as soon as it comes. Thanks a lot already in advance! If you have a chance to test Lumi again and get an error, please let me know what the error message is. Best, Eija From: "Oliver Heil" [ mailto:o....@dk... | <o....@dk...> ] To: "chipster-users" [ mailto:chi...@li... | <chi...@li...> ] Sent: Friday, 25 November, 2022 10:33:14 Subject: Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Hi Eija, yes, I already experimented with Lumi but I got another error (which I can't remember for now), but in general I think it is needed for the other Norm->Illumina tools. Currently I have created a split tool by taking the join tool as a template and it works fine so far. It's still a bit experimental and doc is not yet visible in our chipster installation, but Petri did a great job supporting me with tips. I will finish everything next week. Actually I would do a PR in github but my older PRs are waiting since I made them last year (?) without any discussion, so I am not sure if this the way to provide some contributions. ( [ https://github.com/chipster/chipster-tools/pulls | https://github.com/chipster/chipster-tools/pulls ] ) Regards, Oli Am 25.11.2022 um 08:43 schrieb [ mailto:chi...@cs... | chi...@cs... ] : BQ_BEGIN Hi Oliver, You are right, the former Import tool was replaced in the web based Chipster by the "Convert to Chipster format" option, which allows the user to mark id, sample and other columns, but it doesn't do splitting (people typically use it for RNA-seq count tables). Our Illumina array users use the lumi pipeline which takes a whole file, so it hasn't been a problem. However, if there are users who prefer to use the older Illumina normalization tool, we need to look into this. Making a separate splitting tool like you mentioned might be a better option than modifying the "Convert to Chipster format" functionality, because the latter produces also phenodata and is thus more geared for normalized data. If you want to check out how this system works, select a tsv file, click the three dots after the filename in the File panel and select "Convert to Chipster format". Please let me know what you think and thank you for bringing the problem to our attention! Best, Eija From: "Oliver Heil" [ mailto:o....@dk... | <o....@dk...> ] To: "chipster-users" [ mailto:chi...@li... | <chi...@li...> ] Sent: Wednesday, 23 November, 2022 11:54:37 Subject: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Dear Chipster people, In earlier versions we had the option to import table like data into Chipster via the Import Tool. During which each sample column was created as separate file in Chipster. Tools like "Normalisation" -> "Illumina" expect this type of raw data. With v4 this seems to be a problem now. I can't find anything like the old Import Tool which produces separate Chipster files for each e.g. column in a tab separated .tsv file. In "Misc" -> "Utilitities" there is a "Join tables" but we need a "Split table", isn't it? Any idea how to process old microarray expression data, which is a tab separated file with columns like ProbeID sample1 sample2 sample3 ... ? Regards, Oli -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list [ mailto:Chi...@li... | Chi...@li... ] [ https://lists.sourceforge.net/lists/listinfo/chipster-users | https://lists.sourceforge.net/lists/listinfo/chipster-users ] _______________________________________________ Chipster-users mailing list [ mailto:Chi...@li... | Chi...@li... ] [ https://lists.sourceforge.net/lists/listinfo/chipster-users | https://lists.sourceforge.net/lists/listinfo/chipster-users ] BQ_END _______________________________________________ Chipster-users mailing list [ mailto:Chi...@li... | Chi...@li... ] [ https://lists.sourceforge.net/lists/listinfo/chipster-users | https://lists.sourceforge.net/lists/listinfo/chipster-users ] _______________________________________________ Chipster-users mailing list [ mailto:Chi...@li... | Chi...@li... ] [ https://lists.sourceforge.net/lists/listinfo/chipster-users | https://lists.sourceforge.net/lists/listinfo/chipster-users ] BQ_END -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Oliver H. <o....@dk...> - 2022-11-29 12:55:37
|
Hi Eija, > If you have a chance to test Lumi again and get an error, please let > me know what the error message is. the imported file does not comply to the needed format like column names. So the error is not unexpected. I wanted to show the error anyways (i remember it was rather short) so started a lumi job. This brought chipster now into a bad state: There it is for quite some time now. This is all together not very smooth and expedient but I can't help. I am waiting now until this chipster installation regenerates again. Regards, Oli Am 25.11.2022 um 13:20 schrieb chi...@cs...: > Hi Oliver, > > Thank you for creating the splitting tool. When it is ready and you > have tested it in the DKFZ installation, please make a pull request. > PR in GitHub is indeed the way to go and I have seen the previous ones > (and accepted one of them). I will accept the PR for the splitting > tool as soon as it comes. Thanks a lot already in advance! > > If you have a chance to test Lumi again and get an error, please let > me know what the error message is. > > Best, > Eija > > ------------------------------------------------------------------------ > *From: *"Oliver Heil" <o....@dk...> > *To: *"chipster-users" <chi...@li...> > *Sent: *Friday, 25 November, 2022 10:33:14 > *Subject: *Re: [Chipster-users] Chipster v4 and the Import Tool > (microarray expression data) > > Hi Eija, > > yes, I already experimented with Lumi but I got another error (which > I can't remember for now), but in general I think it is needed for the > other Norm->Illumina tools. > > Currently I have created a split tool by taking the join tool as a > template > and it works fine so far. It's still a bit experimental and doc is not yet > visible in our chipster installation, but Petri did a great job supporting > me with tips. I will finish everything next week. > > Actually I would do a PR in github but my older PRs are waiting since > I made them > last year (?) without any discussion, so I am not sure if this the way to > provide some contributions. > (https://github.com/chipster/chipster-tools/pulls) > > Regards, > > Oli > > Am 25.11.2022 um 08:43 schrieb chi...@cs...: > > Hi Oliver, > > You are right, the former Import tool was replaced in the web > based Chipster by the "Convert to Chipster format" option, which > allows the user to mark id, sample and other columns, but it > doesn't do splitting (people typically use it for RNA-seq count > tables). Our Illumina array users use the lumi pipeline which > takes a whole file, so it hasn't been a problem. However, if there > are users who prefer to use the older Illumina normalization tool, > we need to look into this. > > Making a separate splitting tool like you mentioned might be a > better option than modifying the "Convert to Chipster format" > functionality, because the latter produces also phenodata and is > thus more geared for normalized data. If you want to check out how > this system works, select a tsv file, click the three dots after > the filename in the File panel and select "Convert to Chipster > format". Please let me know what you think and thank you for > bringing the problem to our attention! > > Best, > Eija > > ------------------------------------------------------------------------ > *From: *"Oliver Heil" <o....@dk...> > <mailto:o....@dk...> > *To: *"chipster-users" <chi...@li...> > <mailto:chi...@li...> > *Sent: *Wednesday, 23 November, 2022 11:54:37 > *Subject: *[Chipster-users] Chipster v4 and the Import Tool > (microarray expression data) > > Dear Chipster people, > > In earlier versions we had the option to import table like data into > Chipster via the Import Tool. During which each sample column was > created as separate file in Chipster. Tools like "Normalisation" > -> "Illumina" > expect this type of raw data. > > With v4 this seems to be a problem now. I can't find anything like the > old Import Tool which produces separate Chipster files for each > e.g. column > in a tab separated .tsv file. In "Misc" -> "Utilitities" there is > a "Join tables" but > we need a "Split table", isn't it? > > Any idea how to process old microarray expression data, which is a > tab separated file with columns like > ProbeID sample1 sample2 sample3 ... > ? > > Regards, > > Oli > > -- > > Oliver Heil > Microarray Core Facility > Bioinformatics > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > > o....@dk... <mailto:o....@dk...> > Support: www.dkfz.de/gpcf/phpBB3/index.php > <https://www.dkfz.de/gpcf/phpBB3/index.php> > www.dkfz.de <http://www.dkfz.de> > > Research for a Life without Cancer > > Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
From: <chi...@cs...> - 2022-11-25 12:20:53
|
Hi Oliver, Thank you for creating the splitting tool. When it is ready and you have tested it in the DKFZ installation, please make a pull request. PR in GitHub is indeed the way to go and I have seen the previous ones (and accepted one of them). I will accept the PR for the splitting tool as soon as it comes. Thanks a lot already in advance! If you have a chance to test Lumi again and get an error, please let me know what the error message is. Best, Eija From: "Oliver Heil" <o....@dk...> To: "chipster-users" <chi...@li...> Sent: Friday, 25 November, 2022 10:33:14 Subject: Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Hi Eija, yes, I already experimented with Lumi but I got another error (which I can't remember for now), but in general I think it is needed for the other Norm->Illumina tools. Currently I have created a split tool by taking the join tool as a template and it works fine so far. It's still a bit experimental and doc is not yet visible in our chipster installation, but Petri did a great job supporting me with tips. I will finish everything next week. Actually I would do a PR in github but my older PRs are waiting since I made them last year (?) without any discussion, so I am not sure if this the way to provide some contributions. ( [ https://github.com/chipster/chipster-tools/pulls | https://github.com/chipster/chipster-tools/pulls ] ) Regards, Oli Am 25.11.2022 um 08:43 schrieb [ mailto:chi...@cs... | chi...@cs... ] : Hi Oliver, You are right, the former Import tool was replaced in the web based Chipster by the "Convert to Chipster format" option, which allows the user to mark id, sample and other columns, but it doesn't do splitting (people typically use it for RNA-seq count tables). Our Illumina array users use the lumi pipeline which takes a whole file, so it hasn't been a problem. However, if there are users who prefer to use the older Illumina normalization tool, we need to look into this. Making a separate splitting tool like you mentioned might be a better option than modifying the "Convert to Chipster format" functionality, because the latter produces also phenodata and is thus more geared for normalized data. If you want to check out how this system works, select a tsv file, click the three dots after the filename in the File panel and select "Convert to Chipster format". Please let me know what you think and thank you for bringing the problem to our attention! Best, Eija From: "Oliver Heil" [ mailto:o....@dk... | <o....@dk...> ] To: "chipster-users" [ mailto:chi...@li... | <chi...@li...> ] Sent: Wednesday, 23 November, 2022 11:54:37 Subject: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Dear Chipster people, In earlier versions we had the option to import table like data into Chipster via the Import Tool. During which each sample column was created as separate file in Chipster. Tools like "Normalisation" -> "Illumina" expect this type of raw data. With v4 this seems to be a problem now. I can't find anything like the old Import Tool which produces separate Chipster files for each e.g. column in a tab separated .tsv file. In "Misc" -> "Utilitities" there is a "Join tables" but we need a "Split table", isn't it? Any idea how to process old microarray expression data, which is a tab separated file with columns like ProbeID sample1 sample2 sample3 ... ? Regards, Oli -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list [ mailto:Chi...@li... | Chi...@li... ] [ https://lists.sourceforge.net/lists/listinfo/chipster-users | https://lists.sourceforge.net/lists/listinfo/chipster-users ] _______________________________________________ Chipster-users mailing list [ mailto:Chi...@li... | Chi...@li... ] [ https://lists.sourceforge.net/lists/listinfo/chipster-users | https://lists.sourceforge.net/lists/listinfo/chipster-users ] _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Oliver H. <o....@dk...> - 2022-11-25 08:33:36
|
Hi Eija, yes, I already experimented with Lumi but I got another error (which I can't remember for now), but in general I think it is needed for the other Norm->Illumina tools. Currently I have created a split tool by taking the join tool as a template and it works fine so far. It's still a bit experimental and doc is not yet visible in our chipster installation, but Petri did a great job supporting me with tips. I will finish everything next week. Actually I would do a PR in github but my older PRs are waiting since I made them last year (?) without any discussion, so I am not sure if this the way to provide some contributions. (https://github.com/chipster/chipster-tools/pulls) Regards, Oli Am 25.11.2022 um 08:43 schrieb chi...@cs...: > Hi Oliver, > > You are right, the former Import tool was replaced in the web based Chipster > by the "Convert to Chipster format" option, which allows the user to mark id, > sample and other columns, but it doesn't do splitting (people typically use it > for RNA-seq count tables). Our Illumina array users use the lumi pipeline > which takes a whole file, so it hasn't been a problem. However, if there are > users who prefer to use the older Illumina normalization tool, we need to look > into this. > > Making a separate splitting tool like you mentioned might be a better option > than modifying the "Convert to Chipster format" functionality, because the > latter produces also phenodata and is thus more geared for normalized data. If > you want to check out how this system works, select a tsv file, click the > three dots after the filename in the File panel and select "Convert to > Chipster format". Please let me know what you think and thank you for bringing > the problem to our attention! > > Best, > Eija > > -------------------------------------------------------------------------------- > *From: *"Oliver Heil" <o....@dk...> > *To: *"chipster-users" <chi...@li...> > *Sent: *Wednesday, 23 November, 2022 11:54:37 > *Subject: *[Chipster-users] Chipster v4 and the Import Tool (microarray > expression data) > > Dear Chipster people, > > In earlier versions we had the option to import table like data into > Chipster via the Import Tool. During which each sample column was > created as separate file in Chipster. Tools like "Normalisation" -> "Illumina" > expect this type of raw data. > > With v4 this seems to be a problem now. I can't find anything like the > old Import Tool which produces separate Chipster files for each e.g. column > in a tab separated .tsv file. In "Misc" -> "Utilitities" there is a "Join > tables" but > we need a "Split table", isn't it? > > Any idea how to process old microarray expression data, which is a > tab separated file with columns like > ProbeID sample1 sample2 sample3 ... > ? > > Regards, > > Oli > > -- > > Oliver Heil > Microarray Core Facility > Bioinformatics > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > > o....@dk... <mailto:o....@dk...> > Support: www.dkfz.de/gpcf/phpBB3/index.php > <https://www.dkfz.de/gpcf/phpBB3/index.php> > www.dkfz.de <http://www.dkfz.de> > > Research for a Life without Cancer > > Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: <chi...@cs...> - 2022-11-25 07:43:54
|
Hi Oliver, You are right, the former Import tool was replaced in the web based Chipster by the "Convert to Chipster format" option, which allows the user to mark id, sample and other columns, but it doesn't do splitting (people typically use it for RNA-seq count tables). Our Illumina array users use the lumi pipeline which takes a whole file, so it hasn't been a problem. However, if there are users who prefer to use the older Illumina normalization tool, we need to look into this. Making a separate splitting tool like you mentioned might be a better option than modifying the "Convert to Chipster format" functionality, because the latter produces also phenodata and is thus more geared for normalized data. If you want to check out how this system works, select a tsv file, click the three dots after the filename in the File panel and select "Convert to Chipster format" . Please let me know what you think and thank you for bringing the problem to our attention! Best, Eija From: "Oliver Heil" <o....@dk...> To: "chipster-users" <chi...@li...> Sent: Wednesday, 23 November, 2022 11:54:37 Subject: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data) Dear Chipster people, In earlier versions we had the option to import table like data into Chipster via the Import Tool. During which each sample column was created as separate file in Chipster. Tools like "Normalisation" -> "Illumina" expect this type of raw data. With v4 this seems to be a problem now. I can't find anything like the old Import Tool which produces separate Chipster files for each e.g. column in a tab separated .tsv file. In "Misc" -> "Utilitities" there is a "Join tables" but we need a "Split table", isn't it? Any idea how to process old microarray expression data, which is a tab separated file with columns like ProbeID sample1 sample2 sample3 ... ? Regards, Oli -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Oliver H. <o....@dk...> - 2022-11-23 09:54:50
|
Dear Chipster people, In earlier versions we had the option to import table like data into Chipster via the Import Tool. During which each sample column was created as separate file in Chipster. Tools like "Normalisation" -> "Illumina" expect this type of raw data. With v4 this seems to be a problem now. I can't find anything like the old Import Tool which produces separate Chipster files for each e.g. column in a tab separated .tsv file. In "Misc" -> "Utilitities" there is a "Join tables" but we need a "Split table", isn't it? Any idea how to process old microarray expression data, which is a tab separated file with columns like ProbeID sample1 sample2 sample3 ... ? Regards, Oli -- Oliver Heil Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
From: Chipster <chi...@cs...> - 2022-04-19 07:32:55
|
Hi, that's right. You can get a 3-week evaluation account by sending an email to chi...@cs.... Please see the list of required information for these evaluation account requests on page https://chipster.rahtiapp.fi/access . After the 3 weeks you can either purchase an account to our server (one year personal single user account costs 500 euro for academic use), or setup your own Chipster server (provided you have the necessary IT person and computing resources available). This is our public user support list, but I'll send you soon another email about the Chipster accounts in your organisation. Best regards, Petri / Chipster team > On 15. Apr 2022, at 21.25, pa...@ms... wrote: > > Hi Chipster, > > I am Hyeung Ju Park, Research Associate in Memorial Sloan Kettering. I was wondering if out facility has the access to the Chipster or I should get my own. > I read on your website that non-profit organizations would get 3 weeks free trial. Does it mean after 3 week, a purchase would be necessary to continue to use Chipster? > I will look forward your reply. Thank you. > > Best, > Hyeung Ju Park > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan Kettering Cancer Center may be privileged, confidential, > and protected from disclosure under applicable law. If the reader of > this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, > you are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this message > and deleting this message, any attachments, and all copies and backups > from your computer. > _______________________________________________ > Chipster-users mailing list > Chi...@li... <mailto:Chi...@li...> > https://lists.sourceforge.net/lists/listinfo/chipster-users <https://lists.sourceforge.net/lists/listinfo/chipster-users> |
From: <pa...@ms...> - 2022-04-15 18:43:27
|
Hi Chipster, I am Hyeung Ju Park, Research Associate in Memorial Sloan Kettering. I was wondering if out facility has the access to the Chipster or I should get my own. I read on your website that non-profit organizations would get 3 weeks free trial. Does it mean after 3 week, a purchase would be necessary to continue to use Chipster? I will look forward your reply. Thank you. Best, Hyeung Ju Park ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. |
From: <chi...@cs...> - 2020-10-30 15:38:16
|
Hi all, Please note that the MOOC "Single cell RNA-seq data analysis with Chipster" is now open at [ https://e-learn.csc.fi/course/view.php?id=17 | https://e-learn.csc.fi/course/view.php?id=17 ] . There will be a kick-off webinar on 3.11.2020 at 13:00, please find the details at [ https://ssl.eventilla.com/event/mQKWY | https://ssl.eventilla.com/event/mQKWY ] . The MOOC covers the whole workflow from quality control and normalization to clustering cells and finding marker genes for the clusters. It covers also integrated analysis of two samples and finding conserved markers and cell-type specific expression changes. The MOOC consists of lecture videos, hands-on exercises and questions/tasks. The estimated time to complete the course is 2-3 days. Once you have finished all the tasks, you can download a course certificate with a unique course identifier. In the certificate we recommend granting 1 credit (ECTS) for the course. Best, Eija Eija Korpelainen, Ph.D Product Manager, ELIXIR-FI Training Coordinator CSC - IT Centre for Science P.O.Box 405, 02101 Espoo, Finland Phone +358 50 381 9726 |
From: <chi...@cs...> - 2020-01-31 11:10:46
|
Hi Oliver, for some reason the .md5 files seem to be served with content-type application/x-tar and browsers don't seem to like that. We'll find out why and fix it. For now, curl or wget don't seem to be so picky about it so you could maybe use them. Here are also the contents for http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/3.16.3/tools/tools.tar.gz.md5 5d48bea39bc7fd9bac315782cded7d59 tools.tar.gz Best regards, Taavi / Chipster Team ----- Original Message ----- From: "Oliver Heil" <o....@dk...> To: chi...@li... Sent: Friday, 31 January, 2020 12:27:33 Subject: [Chipster-users] download tools md5 hash Dear Chipster Team, The MD5 hashes of tools.tar.gz at [ http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/ | http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/ ] are unreadable. I just tried to check if my download of version 3.16.3 tools got the complete file without errors but failed because tools.tar.gz.md5 can't be read. regards, Oli -- Oliver Heil GPCF/W110 Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany [ mailto:o....@dk... | o....@dk... ] [ https://www.dkfz.de/gpcf/phpBB3/index.php | Support: www.dkfz.de/gpcf/phpBB3/index.php ] [ http://www.dkfz.de/ | www.dkfz.de ] Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: Oliver H. <o....@dk...> - 2020-01-31 10:27:45
|
Dear Chipster Team, The MD5 hashes of tools.tar.gz at http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/ are unreadable. I just tried to check if my download of version 3.16.3 tools got the complete file without errors but failed because tools.tar.gz.md5 can't be read. regards, Oli -- Oliver Heil GPCF/W110 Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
From: Oliver H. <o....@dk...> - 2020-01-31 10:02:12
|
Dear Aniello, I have added this option to the DKFZ Chipster installation, which I assume you are using. Please try (you have to restart your chipster client) and if something seems to be wrong just send me an email. Regards, Oli Am 30.01.2020 um 13:46 schrieb Federico, Aniello: > > Hi, > > I would like to know if there is the possibility on Chipster to > manually set, during the Affymetrix data normalization (MAS5), the > value at which all arrays will be scaled to. > > By default this value is set to 500; I would need to set it to 100 > instead. > > In R, using the (affy) package, I normally fix the function in this way: > > data.mas5 <-mas5(affy.data,sc=100) > > Thank you in advance. > > Best regards, > > Aniello > > *______________________________________________________* > > *Aniello Federico**, PhD* > > Post-Doc > > Division of Pediatric Neurooncology > > Preclinical Research unit (B062) > > ** > > *Hopp Children’s Cancer Center (KiTZ)* > > ** > > And > > *German Cancer Research Center (DKFZ)* > > Im Neuenheimer Feld 280 > > 69120 Heidelberg > > Tel: +49 6221 42 4623 > > a.f...@dk... <mailto:a.f...@dk...> > > a.f...@ki... <mailto:a.f...@ki...> > > cid:image001.png@01D245B0.8B7A62A0 > > /Users/rode/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1264702104 > > > > _______________________________________________ > Chipster-users mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-users -- Oliver Heil GPCF/W110 Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/phpBB3/index.php <https://www.dkfz.de/gpcf/phpBB3/index.php> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
From: Federico, A. <a.f...@ki...> - 2020-01-30 13:23:20
|
Hi, I would like to know if there is the possibility on Chipster to manually set, during the Affymetrix data normalization (MAS5), the value at which all arrays will be scaled to. By default this value is set to 500; I would need to set it to 100 instead. In R, using the (affy) package, I normally fix the function in this way: data.mas5 <-mas5(affy.data,sc=100) Thank you in advance. Best regards, Aniello ______________________________________________________ Aniello Federico, PhD Post-Doc Division of Pediatric Neurooncology Preclinical Research unit (B062) Hopp Children's Cancer Center (KiTZ) And German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Tel: +49 6221 42 4623 a.f...@dk...<mailto:a.f...@dk...> a.f...@ki...<mailto:a.f...@ki...> [cid:image001.png@01D245B0.8B7A62A0] [/Users/rode/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1264702104] |
From: <chi...@cs...> - 2020-01-29 06:52:20
|
Dear all, Please note that the virtual machine image of Chipster v3.16.3 is now available for download at [ http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/build/3.16.3/ | http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/build/3.16.3/ ] . Should you have any problem updating your Chipster server to this version, please don't hesitate to contact us. This version brings major improvements if compared to Chipster v3.15: -all the single cell RNA-seq analysis tools have been migrated to Seurat v3 and R3.6.1 -a bug in HISAT2 aligners affecting downstream analysis with Cufflinks and Cuffdiff has been fixed (please refer your users to [ https://chipster.csc.fi/manual/newVersion.html | https://chipster.csc.fi/manual/newVersion.html ] for details) Best, Eija and the Chipster team Eija Korpelainen, Ph.D Product Manager CSC - IT Centre for Science P.O.Box 405, 02101 Espoo, Finland Phone +358 50 381 9726 |
From: <chi...@cs...> - 2020-01-27 06:35:31
|
Dear Adnan, The Chipster software is free of charge. It is a client-server system and we have packaged the whole thing as a virtual machine image (VMI) so that it is easier to set the server up. The VMI is available at [ https://chipster.github.io/chipster/ | https://chipster.github.io/chipster/. ] Please note that we will release a new version (3.16.3) this week, so we advice you to wait for that. For users who don't have sufficient computing resources or technical support in their institute to set up their own server, we offer a possibility to use our Chipster server in Finland (https://chipster.csc.fi/). In this case we need to charge you for computing resources 500 euros/year, as we are a computing center for the Finnish universities owned by the Ministery of Education. However, we do provide 3-week evaluation accounts for free so that people can test Chipster before deciding to set up their own server. When you say that you downloaded Chipster to your laptop, do you mean that downloaded the whole VMI from [ https://chipster.github.io/chipster/ | https://chipster.github.io/chipster/ ] (so that you actually run Chipster server on your laptop), or did you click on the Launch link at https://chipster.csc.fi/ (so you have just the Chipster client program on your laptop)? If the latter, you need to get access to our server, please see the instructions at [ https://chipster.csc.fi/access.shtml | https://chipster.csc.fi/access.shtml ] . Best, Eija From: "lahuf aa" <lah...@ou...> To: "chipster-users" <chi...@li...> Sent: Saturday, 25 January, 2020 22:58:39 Subject: [Chipster-users] Creat Chipster account Dear Sir/Madam, I am so interesting in utilizing Chipster. Thus I downloaded it in my Laptop. However, when I have tried to create Chipster account nothing coming up. Therefore, I would like to ask is the Chipster is free or I need to purchase the license. Please inform me asap. Regards Adnan _______________________________________________ Chipster-users mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-users |
From: <lah...@ou...> - 2020-01-25 20:58:53
|
Dear Sir/Madam, I am so interesting in utilizing Chipster. Thus I downloaded it in my Laptop. However, when I have tried to create Chipster account nothing coming up. Therefore, I would like to ask is the Chipster is free or I need to purchase the license. Please inform me asap. Regards Adnan |