ExpressionFileCreator cannot generate the GCT file

[parin....@gmail.com]

Please respond with the following information as applicable:
 Complete description of the problem (ie what you were trying to do and what went wrong): I want to generate a RES or GCT file from a set of Affymetrix CEL files. I upload the CEL files and CDF file for run analysis. Finally, The job finished without an error but I get only stdout.txt file that detailed about an error of No annotations found for chip Clariom_S_Human.

Job ID if run on a publicly available server. The job ID is 1639851. ExpressionFileCreator

[srilaksh...@gmail.com]

HIi, did you get a response from GP help for this problem?

I can't even access expression file creator. WOuld you mind advising me how you did it?

Thanks

Sri

[Barbara Hill]

Hello Sri, 

Can you explain what you mean by "I can't even access expression file creator. "?

Best

-Barbara

[srilakshmi sharma]

Dear Barbara

Thanks so much for contacting me. I was beginning to lose hope!

The current online version of gene pattern does not permit me to convert IVT (Affymetrix) array  CEL files . It only allows ST arrays

Therefore, it is suggested that I download an older version of genepattern in order to find expression file creator somewhere in that package.

On attempting to do open a genepattern dated from 2017 or even earlier, the package downloads to my Macbook and then asks me to register which I duly do and then asks me to re-open gene pattern When I attempt to open gene pattern, it opens a browser page ( firefox) but I get a completely blank screen. 

There is no facility to open an older version of genepattern without the internet. 

Please note, the only reason I am trying to download genepattern is because I need to use expression file creator to make GCT files from my CEL files and utilise GSEA using my data

Thank you for your kind attention to this issue. I apologise for not being more computer savvy

Sri

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[Barbara Hill]

Hello Sri, 

Several of us were away on vacation, hence the delay. Our apologies.

I sent links to the module you are looking for - you do not need to run it on your own server.

https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/genepattern-help/eNJqp0Mmzfs

Please let me know if that does not answer your questions.

Best

-Barbara

[srilakshmi sharma]

Thanks so much Barbara

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