Re: [Chipster-users] Chipster v4 and the Import Tool (microarray expression data)

[Oliver H. <o....@dk...>]

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
>
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