Activity for COHCAP
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Charles Warden posted a comment on discussion GitHub-Only Version for Bioconductor Code
The requested end date to work in the Integrative Genomics Core at City of Hope for the developer (Charles Warden) is 4/30/2024, where he will then enroll in the "Genetics, Genomics, and Bioinformatics" PhD program at UC-Riverside. While some support was provided when he was at the University of Michigan, there was discussion about how the transition plan could be improved during this time of change. After discussions, the decision was made to actively request that the Bioconductor version be retired,...
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Hi Diraj, I have started a GitHub issue for the topic of parameter troubleshooting: https://github.com/cwarden45/COHCAP/issues/4 Please continue the discussion on GitHub. Thank you very much for your interest in using COHCAP! Sincerely, Charles
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Anonymous posted a comment on discussion Bioconductor Issues
Hi Charles, Thank you so much for your response, I havwe made osme changes in S3 file and removed metastatic (2) from sample file. So now the Sample file has only 2 groups i,e primary and solid tisssue normal. Now the code is : dir = "/Users/dkaur/Desktop/HNSC/COHCAP/Files" beta.file = file.path(dir,"S3.txt") sample.file = file.path(dir,"Sample_HNSC.txt") expression.file = file.path(dir,"expression-Average_by_Island.txt") project.folder = "/Users/dkaur/Desktop/HNSC/" project.name = "HNSC-SUB" code...
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I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...
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I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...
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I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...
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I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...
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I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...
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I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores. 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the normal group would be...
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I believe that there are at least 2 problems. To describe the first problem, there was a tab in the last line of the sample description file. This caused the program to expect an additional sample that was not present. I have updated that modified file. This causes the following substitution in the code provided above: sample.file = "Sample_HNSC--NO_TAB.txt" That then results in the following messages: Loading required package: WriteXLS Loading required package: COHCAPanno Loading required package:...
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Hi Dilraj, If you post content here, I don't think you have to post the exact same content in the GitHub disucssion group. However, if somebody else (Nitish) started this particular post, then I think new posts should start on GitHub (or at least be a new post within this group). If there was only 1 post (and my response), then I think that could be coped to GitHub (with a note to mention the discussion will be continued there). Or, I could have started a new post on GitHub, summarizing the previous...
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Anonymous posted a comment on discussion Bioconductor Issues
Hi Charles, Thank you for your response. Yes i am using Bioconductor COHCAP. I have made 3 input files one is S3. txt similar to GSE42308_truncated.txt, Sample_HNSC.txt similar to sample_GSE42308.txt and one is HNSC-gene expression dataset similar to expression-Average_by_Island_truncated.txt consisting of Genes and TCGA sample ids. I have done the annotation part, but when it comes to the cpg site function, it throws this error. The sample file has 3 groups Primary tumor (528), solid normal (50)...
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Hi, I apologize, but I think data from the Dropbox link may be too large for me to provide assistance through the on-line support system. I believe the use of the S3.txt and Sample_HNSC.txt files is a good idea. However, I have the following questions: 1) Are you using the standalone version of COHCAP (hosted here) or the Bioconductor version of COHCAP (currently, available here). I would recommend using the Bioconductor version. If you are the same individual with the earlier question, then I can...
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Anonymous posted a comment on discussion Bioconductor Issues
Hi Charles, I am working on TCGA-HNSC methylation datset having 580 samples. The annotation part is working fine and i am able to generate Beta table but, i am facing error with COHCAP.site. Error in COHCAP.site(sample.file, beta.table, project.name, project.folder, : In addition: Warning messages: 1: In COHCAP.site(sample.file, beta.table, project.name, project.folder, : Some samples in sample description file are not present in the beta file! 2: In COHCAP.site(sample.file, beta.table, project.name,...
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Anonymous posted a comment on discussion Bioconductor Issues
Hi Charles, I am working on TCGA-HNSC methylation datset having 580 samples. The annotation part is working fine and i am able to generate Beta table but, i am facing error with COHCAP.site. Error in COHCAP.site(sample.file, beta.table, project.name, project.folder, : In addition: Warning messages: 1: In COHCAP.site(sample.file, beta.table, project.name, project.folder, : Some samples in sample description file are not present in the beta file! 2: In COHCAP.site(sample.file, beta.table, project.name,...
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COHCAP released /cohcap-v-1.3.2.zip
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Do you have a demo dataset?
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Do you have a demo dataset?
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Do you have a demo dataset?
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Do you have a demo dataset?
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Do you have a demo dataset?
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Anonymous posted a comment on discussion Bioconductor Issues
Thank you for your reply, Charles. Firstly, I have two expression files prepared - one for "by site workflow" and second for the "by island" workflow. I also did follow the necessary steps for both of the workflows. Unfortunately, nothing was really helping with my "COHCAP.integrate.avg.by.island" error that I was constantly getting. I wanted to compare the result from both functions. But it seems in the meanwhile I've fixed this issue. The problem was following: in all of the other files including...
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Hi Joanna, I think the issue is that only certain fuctions can be used together: So, COHCAP.integrate.avg.by.site() has to be used after COHCAP.avg.by.site(), and COHCAP.integrate.avg.by.island() has to be used after COHCAP.avg.by.island(). For the Average-by-Site workflow, the expression file doesn't have any sample names (just a fold-change value, p-value, and FDR value). I've attached copies of the demo expression files for the Bioconductor version. So, if using the Average-by-Site workflow, please...
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Anonymous posted a comment on discussion Bioconductor Issues
Hello, I'm using COHCAP to correlate my methylation data with the expression data. Everything looks fine when I'm using "by site" workflow but when I want to integrate by island I'm constantly getting the same error suggesting that my expression file does not contain any of my samples. It seems like it writes a warning about all the sample names missing in expression file and then produces NAs ("X9_13 not found in expression file, so all values will be set to 'NA'"), then the NAs are ommited and...
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How do I create a new .jar file for my platform?
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How do I create a new .jar file for my platform?
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How do I create a new .jar file for my platform?
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Hi Shib, To be honest, most updates have been in the Bioconductor version rather than the standalone version: https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html So, if you are still encountering problems, you may want to consider using that version. However, I am going to try and help you solve this particular problem: I think the issue may be that you have a space in your folder name in the path to the parameter file (the name of the folder where you are running COHCAP). For example,...
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How do I create a new .jar file for my platform?
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How do I create a new .jar file for my platform?
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Home
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Anonymous posted a comment on discussion General Discussion
HI, I am using cohcap gui in windows 7, 64 bit pc, after installing all the required things (JDK, pearl) for running cohcap gui, I am getting error message like this. I am getting this error on the test datasets provided for help. Uncaught exception from user code: Could not open C:\Users\SHIB! at cohcap.pl line 187. main::run_cohcap("C:\Users\SHIB", "PC", "F:\METHYL~1\COHCAP\COHCAP~1.1\bin\", 1, 1, 1, 1, 1, ...) called at cohcap.pl line 122 Please help me to overcome from this problem, Thanks Shib...
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Hi, That looks correct in terms of the number of columns (assuming there is a new line between the header and the first data row, and you have a tab-delimited text file). However, you're going to encounter problems with "+" and "-" in the sample names. So, please change them to something like "pos" and "neg". As an example, I've tested running analysis up to the site step without any problems (after creating a folder called "Example", where I want to save the results), using the attached files. That...
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Anonymous posted a comment on discussion General Discussion
"SiteID" "M70-_1" "M70+_1" "P70-_1" "P70+_1" "M70-_2" "M70+_2" "P70-_2" "P70+_2" "cg00000957" 0.88187134502924 0.873669688608593 0.892410191770955 0.909056316590563 0.925964912280702 0.917353173039023 0.937030701359503 0.954509132420091
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Can you please provide the first few lines of 'myDatafile'? Also, is the MyNormFile object being created with this command? MyNormFile = read.table(myDatafile, header = T, sep = "\t") There aren't supposed to be any row names imported (in COHCAP). I would guess the number of values in the header varies from the number of columns in the data frame (although R has a separate error message for that, and I wouldn't expect SiteID to have the correct probe IDs if that column was incorrectly being used...
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Anonymous posted a comment on discussion General Discussion
beta.table = COHCAP.annotate(myDatafile, "MyMethylation", project.folder, + platform="450k-UCSC") which gives: Error in read.table(beta.file, header = T, sep = "\t") : duplicate 'row.names' are not allowed check SiteID which suppose to be the row.names with: anyDuplicated(MyNormFile$SiteID) and show: [1] 0 There are no duplication
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Anonymous posted a comment on discussion General Discussion
Hello Charles, Thank you so much for your answer. Take care and Happy new year, JK
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Hi JK, In most cases, I would recommend using the "Average-by-Island" results. Both workflows have the same site-level analysis, but differ in how differentially methylated islands are defined from the differentially methylated sites. The "Average-by-Island" workflow averages methylation values across differentially methylated sites within an annotated region (assuming that there are a minimum number of differentially methylated sites, which by default is 4). This defines one methylation value per...
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Anonymous posted a comment on discussion General Discussion
Hello, I am doing some NGS methylation project with COHCAP and I am quite happy with it. Thank you. I have a question though. I read the documents and ran COHCAP.avg.by.site and COHCAP.avg.by.island, but I am confused with which results I should use for my project. what I want to know is differentially methylated islands, but it seems like both of the results have differentially methylated islands. Here is my results. Avg_by_Site www.dropbox.com/s/zd5v9fmvw2gmn7o/CpG_Island_filtered-Avg_by_Site.JPG?dl=0...
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James Askew posted a comment on discussion General Discussion
Was never very good about proofing txt files to see if there are any extra charaters. That was the trick and my data set ran to completion. I thank you for your help in analyzing my data, and wish you happy holidays! James
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Hi James, You have to use a sample description file where all the samples have metadata (if you methylation table has extra samples, then that is OK; they will just not be used in the analysis). That said, there were two extra tabs on line 70 in the file where I removed the incomplete rows, so an empty line may be considered as having a factor of "" (no value, but not set as NA). I've attached a copy of the sample description file where those extra tabs are cleaned (and there are no samples without...
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Ran your script with a couple of changes: - WriteXLSX.pl does not currently work on my computer, so I changed output to txt. - changed the name of the sample.file in script to COHCAP.sample.file And I get the following error message: james@james-OptiPlex-990:~/Documents/COHCAP/cohcap-v-1.3.1/data$ Rscript run_COHCAP3.R Loading required package: WriteXLS Loading required package: COHCAPanno Loading required package: RColorBrewer Loading required package: gplots Attaching package: ‘gplots’ The following...
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Hi James, I would expect the commands in the attached file should at least run without errors (as along as there are enough sites identified for island-level analysis). Best Wishes, Charles
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Hi James, I can't really tell which samples are supposed to come from related twins (and the number of mutant/parental labels isn't equal, so most samples don't have samples for both twins). However, I've attached a sample description file, where I've filled in a Twin ID column with a value in increasing order (although I doubt the values that I filled in are 100% correct, since the mutant/parental labels are not in always in the same order). Best Wishes, Charles
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Hi James, I can't really tell which samples are supposed to come from related twins (and the number of mutant/parental labels isn't equal, so most samples don't have samples for both twins). However, I've attached a sample description file, where I've filled in a Twin ID column with a value in increasing order (although I doubt the values that I filled in are 100% correct, since the mutant/parental labels are not in always in the same order). Best Wishes, Charles
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Charles, Here's an example of the samples file I hope to use for Average-by-Island workflow. Can you use this as an example of setting up the twins for anaylsis? My email is jwaskew@unmc.edu so feel free to use that if you wish. James
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Hi James, I'm afraid that I no longer have your e-mail with your data (and I also cleaned up my hard drive on my computer), so it is difficult for me to directly give you an example with your samples. However, the analysis of the TCGA tumor vs normal data in the COHCAP paper was paired, and that example dataset (with results) is still available (http://bravo.coh.org/COHCAP/Paired_TCGA_Data.tar.gz). That file is quite large, so I've attached the sample description file for that analysis (sample_tumor_vs_normal_filtered_paired.txt),...
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Hi James, I'm afraid that I no longer have your e-mail with your data (and I also cleaned up my hard drive on my computer), so it is difficult for me to directly give you an example with your samples. However, the analysis of the TCGA tumor vs normal data in the COHCAP paper was paired, and that example dataset (with results) is still available (http://bravo.coh.org/COHCAP/Paired_TCGA_Data.tar.gz). That file is quite large, so I've attached the sample description file for that analysis (since that...
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Hi James, Sorry for the delayed response - there were a couple issues: 1) In the Bioconductor version, the COHCAP.annotate() function strictly requires that the probe ID be in a column named "SiteID" (not TargetID) 2) There is still some issue with the compatibilty of the sample names. However, if you use descriptive names (such as Sample1, Sample2) in the sample description file and beta table, that will work. If those changes are made, the following commands can produce some differentially methylated...
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I'll look in to running all my samples through your Average-by-Island workflow. Can you give me an idea of what to put in the sample description table to identify samples as twin pairs? You mentioned adding another column, but I can't seem to figure out how to identify samples as twin pairs in this new column. Thanks, James
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Hi James, If every twin pair has one affected and one unaffected individual, you can analyze all the samples at the same time and specify some sort of twin ID as the pairing variable. While COHCAP does provide a way to run a 1-vs-1 comparison (with the Average-by-Site workflow), I would recommend maximizing the number of samples that you compare and use the Average-by-Island workflow (which is used with the example code in the COHCAP vignette). To specify a special pairing variable, you'll add another...
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Hi, I am not sure what is causing this issue. While I admittedly started testing EPIC data with the standalone version of COHCAP, I would currently use the Bioconductor version for analysis. If you're using a Linux computer, I haven't tested the GUI on Linux, but I know the Bioconductor version of COHCAP works on Linux. To use the Bioconductor version of COHCAP with an EPIC array, there are two parameters to use for the COHCAP.annotate() function: 1) platform="custom" 2) annotation.file = [name of...
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uHi, I am not sure what is causing this issue. While I admittedly started testing EPIC data with the standalone version of COHCAP, I would currently use the Bioconductor version for analysis. If you're using a Linux computer, I haven't tested the GUI on Linux, but I know the Bioconductor version of COHCAP works on Linux. To use the Bioconductor version of COHCAP with an EPIC array, there are two parameters to use for the COHCAP.annotate() function: 1) platform="custom" 2) annotation.file = [name...
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uHi, I am not sure what is causing this issue. While I admittedly started testing EPIC data with the standalone version of COHCAP, I would currently use the Bioconductor version for analysis. If you're using a Linx computer, I haven't tested the GUI on Linux, but I know the Bioconductor version of COHCAP works on Linux. To use the Bioconductor version of COHCAP with an EPIC array, there are two parameters to use for the COHCAP.annotate() function: 1) platform="custom" 2) annotation.file = [name of...
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Hi James, If every twin pair has one affected and one unaffected individual, you can analyze all the samples at the same time and specify some sort of twin ID as the pairing variable. While COHCAP does provide a way to run a 1-vs-1 comparison (with the Average-by-Site workflow), I would recommend maximizing the number of samples that you compare and use the Average-by-Island workflow (which is used with the example code in the COHCAP vignette). To specify a special pairing variable, you'll add another...
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Charles, We've run our discordant twins through COHCAP for the disease we're looking at. I am curious to know if we can rule out a CpG island as a disease causing candidate if we are seeing both increased methylation and decreased methylation across families at a single site. We've a few CpG islands showing signficant methylation changes for more than one family. However these sites are showing both increased and decreased methylation. In your opinion, does this rule out these site as viable candidates...
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Hi, The 1st column in the beta file should be the probeID (with the column labeled "SiteID"). After that, there is one column per sample). These beta values can come from minfi or GenomeStudio. There is a small example file within the COHCAP package: dir = system.file("extdata", package="COHCAP") beta.file = file.path(dir,"GSE42308_truncated.txt") test = read.table(beta.file, head=T, sep="\t") However, please note that the input to COHCAP is the tab-delimited text file (not the data frame, which...
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Anonymous posted a comment on discussion Bioconductor Issues
beta.table = COHCAP.annotate(beta.file, project.name, project.folder, + platform="450k-UCSC") how to prepare beta.file?
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Hi James, You are very welcome! Thanks, Charles
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Charles, COHCAP has been working great. I want to thank you for the help in getting it up and running with my data sets. James
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Hi James, 1) If you are running the scripts interactively with R, you can use ? or help() to learn more about the functions. For example, ?COHCAP.site will tell you more about the COHCAP.site() function. There is a num.groups parameter, which by default is set to num.groups=2. However, you can set the number of groups to other values such as 3 or 1 (although I don't typically do that, so those functions may be subject less debugging than the most commonly used sets of parameters). 2) While some updates...
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Hi James, 1) If you are running the scripts interactively with R, you can use ? or help() to learn more about the functions. For example, ?COHCAP.site will tell you more about the COHCAP.site() function. There is a num.groups parameter, which by default is set to num.groups=2. However, you can set the number of groups to other values such as 3 or 1 (although I don't typically do that, so those functions may be subject less debugging than the most commonly used sets of parameters). 2) While some updates...
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On another note, should I worry about a post site analysis saying "unmethyl.cutoff > methyl.cutoff"?
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With all you've given me for steps, it seem to be working with the new data sets I'm running. Curious to know if I can change the number of groups that I analyze. I tried using a third group in the sample file, but COHCAP errored out and stated: "There are 3 but user specified algorithm for 2 groups." Can I increase the number for the algorithm to 3? Thanks, James
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Hi James, Sorry for the delayed response - there were a couple issues: 1) In the Bioconductor version, the COHCAP.annotate() function strictly requires that the probe ID be in a column named "SiteID" (not TargetID) 2) There is still some issue with the compatibilty of the sample samples. However, if you use descriptive names (such as Sample1, Sample2) in the sample description file and beta table, that will work. If those changes are made, the following commands can produce some differentially methylated...
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Hi James, Sorry for the delayed response - there were a couple issues: 1) In the Bioconductor version, the COHCAP.annotate() function strictly requires that the probe ID be in a column named "SiteID" (not TargetID) 2) There is still some issue with the compatibilty of the sample samples. However, if you use descriptive names (such as Sample1, Sample2) in the sample description file and beta table, that will work. If those changes are made, the following commands can produce some differentially methylated...
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Hi James, Sorry for the delayed response - there were a couple issues: 1) In the Bioconductor version, the COHCAP.annotate() function strictly requires that the probe ID be in a column named "SiteID" (not TargetID) 2) There is still some issue with the compatibilty of the sample samples. However, if you use descriptive names (such as Sample1, Sample2) in the sample description file and beta table, that will work. If those changes are made, the following commands can produce some differentially methylated...
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Hi James, To be honest, I don't use the COHCAP.qc() function myself. I would either have some scripts to create QC figures from the input, which vary from case-to-case, or I have COHCAP create .txt files that I can parse after it runs (using output.format = "txt"). So, the short answer is that you can skip that function. I'll make a note to remove that from the vignette, although I don't want to completely get rid of the function. That said, the number of NA values should be less than 1% per sample,...
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Hi James, Something went wrong with the annotation step. I'm also a bit confused because I thought that you had 8 samples (if you don't have replicates, you'll probably want to deviate from the standard COHCAP pipeline; for example, you'll need to set "fdr.cutoff=1, pvalue.cutoff=1" for COHCAP.site()). However, let's get the annotation step working first. Is it possible for you to send me a copy of your input file of beta value to cwarden45@gmail.com or post the first few lines of the input file...
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Here's results from head(beta.table): head(beta.table) [1] SiteID Chr [3] Loc Gene [5] Island X200848860101_R02C01.AVG_Beta [7] X200848860143_R02C01.AVG_Beta <0 rows> (or 0-length row.names) And this is after changing the samples table to: X200848860101_R02C01.AVG_beta parental X200848860143_R02C01.AVG_beta mutant From the beta.table, am I to assume my data has no annotated beta values? I have to say I'm a little perplexed. COHCAP seems to be doing what it's supposed to do, as you saw from the results...
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Hi James, There are discrepancies between the sample labels in the beta.table and your sample description file - possibly introduced when creating a data frame in R. I believe I've written the code to handle the most common issue (when the chip IDs are used as the same names, an X has to be added to the beginning of the name that starts with a number), but the safest solution is to use the exact name that you see in the beta table. So, if your COHCAP.annotate command looks something like this: beta.table...
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Hi James, There are discrepancies between the sample labels in the beta.table and your sample description file - possibly introduced when creating a data frame in R. I believe I've written the code to handle the most common issue (when the chip IDs are used as the same names, an X has to be added to the beginning of the name that starts with a number), but the safest solution is to use the exact name that you see in the beta table. So, if your COHCAP.annotate command looks something like this: beta.table...
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Hi James, There are discrepancies between the sample labels in the beta.table and your sample description file - possibly introduced when creating a data frame in R. I believe I've written the code to handle the most common issue (when the chip IDs are used as the same names, an X has to be added to the beginning of the name that starts with a number), but the safest solution is to use the exact name that you see in the beta table. So, if your COHCAP.annotate command looks something like this: beta.table...
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Hi James, There are discrepancies between the sample labels in the beta.table and your sample description file - possibly introduced when creating a data frame in R. I believe I've written the code to handle the most common issue (when the chip IDs are used as the same names, an X has to be added to the beginning of the name that starts with a number), but the safest solution is to use the exact name that you see in the beta table. So, if your COHCAP.annotate command looks something like this: beta.table...
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Hi James, There are discrepancies between the sample labels in the beta.table and your sample description file - possibly introduced when creating a data frame in R. I believe I've written the code to handle the most common issue (when the chip IDs are used as the same names, an X has to be added to the beginning of the name that starts with a number), but the safest solution is to use the exact name that you see in the beta table. So, if your COHCAP.annotate command looks something like this: beta.table...
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Hi James, There are discrepancies between the sample labels in the beta.table and your sample description file - possibly introduced when creating a data frame in R. I believe I've written the code to handle the most common issue (when the chip IDs are used as the same names, an X has to be added to the beginning of the name that starts with a number), but the safest solution is to use the exact name that you see in the beta table. So, if your COHCAP.annotate command looks something like this: beta.table...
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Charles, Was able to get a subset of samples to annotate. But would like to know what this following message means when attempting to do CpG site analysis: 1: In COHCAP.site(sample.file, beta.table, project.name, project.folder, : Some samples in sample description file are not present in the beta file! 2: In COHCAP.site(sample.file, beta.table, project.name, project.folder, : 8 items in sample description file 3: In COHCAP.site(sample.file, beta.table, project.name, project.folder, : 8 items in...
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Hi James, To be honest, I don't use the COHCAP.qc() function myself. I would either have some scripts to create QC figures from the input, which vary from case-to-case, or I have COHCAP create .txt files that I can parse after it runs (usingoutput.format = "txt"). So, the short answer is that you can skip that function. I'll make a note to remove that from the vignette, although I don't want to completely get rid of the function. That said, the number of NA values should be less than 1% per sample,...
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Hi James, To be honest, I don't use the COHCAP.qc() function myself. I would either have some scripts to create QC figures from the input, which vary from case-to-case, or I have COHCAP create .txt files that I can parse after it runs (usingoutput.format = "txt"). So, the short answer is that you can skip that function. I'll make a note to remove that from the vignette, although I don't want to completely get rid of the function. That said, the number of NA values should be less than 1% per sample,...
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Hi James, To be honest, I don't use the COHCAP.qc() function myself. I would either have some scripts to create QC figures from the input, which vary from case-to-case, or I have COHCAP create .txt files that I can parse after it runs (usingoutput.format = "txt"). So, the short answer is that you can skip that function. I'll make a note to remove that from the vignette, although I don't want to completely get rid of the function. That said, the number of NA values should be less than 1% per sample,...
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Hi James, To be honest, I don't use the COHCAP.qc() function myself. I would either have some scripts to create QC figures from the input, which vary from case-to-case, or I have COHCAP create .txt files that I can parse after it runs (using output.format = "txt"). So, the short answer is that you can skip that function. I'll make a note to remove that from the vignette, although I don't want to completely get rid of the function. That said, the number of NA values should be less than 1% per sample,...
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Hi James, To be honest, I don't use the COHCAP.qc() function myself. I would either have some scripts to create QC figures from the input, which vary from case-to-case, or I have COHCAP create .txt files that I can parse after it runs (using output.format = "txt"). So, the short answer is that you can skip that function. I'll make a note to remove that from the vignette, although I don't want to completely get rid of the function. That said, the number of NA values should be less than 1% per sample,...
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Anonymous posted a comment on discussion General Discussion
That was very helpful! Thanks again. Was able to annotate the files I mentioned earlier. Got: [1] 866895 9 [1] "Using custom island/gene annotations from : COHCAP_EPIC_UCSC_TSS1500_plus_1st_Exon.txt" [1] 866895 5 [1] 0 5 [1] 0 13 However, when running: COHCAP.qc(sample.file, beta.table, project.name, project.folder) command line I get the following message: Error in FUN(X[[i]], ...) only defined in a data frame with all numeric variables. If I understand this correctly, I have a non-numeric value...
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Hi James, The standalone version was designed for the GenomeStudio output, where your format should match the example file GSE42308.txt in the "data\array_integration" subfolder. If you export a table like the sample file (for example, don't export both average beta and detection p-values), you can create a file for the Bioconductor version in R as follows: input.table = read.table("FinalReport.txt", head=T, sep="\t", skip=8) input.table = input.table[,-ncol(input.table)] write.table(input.table,"Bioconductor_input.txt",...
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Hi James, The standalone version was designed for the GenomeStudio output, where your format should match the example file GSE42308.txt in the "data\array_integration" subfolder. If you export the average beta and detection p-values, the code would be a little complicated; however, if you export a table like the sample file, you can create a file for the Bioconductor version in R as follows: input.table = read.table("FinalReport.txt", head=T, sep="\t", skip=8) input.table = input.table[,-ncol(input.table)]...
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Hi James, The standalone version was designed for the GenomeStudio output, where your format should match the example file GSE42308.txt in the "data\array_integration" subfolder. If you export the average beta and detection p-values, the code would be a little complicated; however, if you export a table like the sample file, you can create a file for the Bioconductor version in R as follows: **1) Import using input.table = read.table("FinalReport.txt", head=T, sep="\t", skip=8) 2) Remove the last...
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Hi James, The standalone version was designed for the GenomeStudio output, where your format should match the example file GSE42308.txt in the "data\array_integration" subfolder. If you export the average beta and detection p-values, the code would be a little complicated; however, if you export a table like the sample file, you can create a file for the Bioconductor version in R as follows: 1) Import using input.table = read.table("FinalReport.txt", head=T, sep="\t", skip=8) 2) Remove the last empty...
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Hi James, The standalone version was designed for the GenomeStudio output, where your format should match the example file GSE42308.txt in the "data\array_integration" subfolder. If you export the average beta and detection p-values, the code would be a little complicated; however, if you export a table like the sample file, you can create a file for the Bioconductor version in R as follows: 1) Import using input.table = read.table("FinalReport.txt", head=T, sep="\t", skip=8) 2) Remove the last empty...
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Hi James, The standalone version was designed for the GenomeStudio output, where your format should match the example file GSE42308.txt in the "data\array_integration" subfolder. If you export the average beta and detection p-values, the code would be a little complicated; however, if you export a table like the sample file, you can create a file for the Bioconductor version in R using input.table = read.table("FinalReport.txt", head=T, sep="\t", skip=8), input.table = input.table[,-ncol(input.table)]...
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Charles, Have been having trouble with the table of beta values I am generating from Genome Studio version 2011.1.0.24550. When creating this final report I am not able to select any boxes from the columns or subcolumns sections when only Sample Methylation Profile is selected. Only way I can select the items you indicated on your input files pdf is by selecting Group Methylation Profile too. Is this creating a txt table with unwanted formatting that COHCAP won't read? I could send you the file but...
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Anonymous posted a comment on discussion General Discussion
Much thanks Charles! I appreciate the advice but am a novice COHCAP user and will see if I can get this to work. James
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Hi, I am not sure what is causing this issue. While I admittedly started testing EPIC data with the standalone version of COHCAP, I would currently use the Bioconductor version for analysis. If you're using a Linx computer, I haven't tested the GUI on Linux, but I know the Bioconductor version of COHCAP works on Linux. To use the Bioconductor version of COHCAP with an EPIC array, there are two parameters to use for the COHCAP.annotate() function: 1) platform="custom" 2) annotation.file = [name of...
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Hi, I am not sure what is causing this issue. While I admittedly started testing EPIC data with the standalone version of COHCAP, I would currently use the Bioconductor version for analysis. If you're using a Linx computer, I haven't tested the GUI on Linux, but I know the Bioconductor version of COHCAP works on Linux. To use the Bioconductor version of COHCAP with an EPIC array, there are two parameters to use for the COHCAP.annotate() function: 1) platform="custom" 2) annotation.file = [name of...
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Hi, I am not sure what is causing this issue. While I admittedly started testing EPIC data with the standalone version of COHCAP, I would currently use the Bioconductor version for analysis. If you're using a Linx computer, I haven't tested the GUI on Linux, but I know the Bioconductor version of COHCAP works on Linux. To use the Bioconductor version of COHCAP with an EPIC array, there are two parameters to use for the COHCAP.annotate() function: 1) platform="custom" 2) annotation.file = [name of...
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Anonymous posted a comment on discussion General Discussion
I have this error message while running cohcapGUI analysis on EPIC data. Wondering if someone might be able to shed some light for me on what is going on. /home/james/Downloads/cohcap-v-1.3.1/bin/R/CpG_Island.R: 3: /home/james/Downloads/cohcap-v-1.3.1/bin/R/CpG_Island.R: : not found /home/james/Downloads/cohcap-v-1.3.1/bin/R/CpG_Island.R: 4: /home/james/Downloads/cohcap-v-1.3.1/bin/R/CpG_Island.R: Syntax error: "(" unexpected /home/james/Downloads/cohcap-v-1.3.1/bin/R/CpG_Island.R: 3: /home/james/Downloads/cohcap-v-1.3.1/bin/R/CpG_Island.R:...
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It looks like you already have some other assistance / knowledge about data analysis, but I'm afraid I can't help you troubleshoot. Best of luck to you!
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Anonymous posted a comment on discussion General Discussion
Hi Charles, Thank you for your answer. I have tried methyl.cutoff=0, unmethyl.cutoff = 1 but still the results are same even when tried on a different BS data, see output here: > filtered.sites <- COHCAP.site(sample.file, beta.table, project.name, project.folder, ref="Control", methyl.cutoff=0, unmethyl.cutoff = 1, paired=FALSE,fdr.cutoff=1, num.groups=2, plot.heatmap=TRUE, output.format = "txt")[1] "Reading Sample Description File...." [1] 396600 82 [1] 396600 82 [1] "Differential Methylation Stats...
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I'm sorry - I provided the opposite methyl / unmethyl thresholds. You need to set methyl.cutoff=0, unmethyl.cutoff = 1 (assuming setting both values to 0.3 doesn't work). Those cutoffs would usually be to check that the methylation state has changed (in one group, beta is above methylated cutoff, and in the other group, beta is less than the unmethylated cutoff). That said, it looks like you've figured that out with the 2nd part of your code If you still aren't identifying any regions, there may...
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