Re: [genepattern-help:3034] Re: DeSeq2 job error RNAseq Raw readcount

[Ted Liefeld]

Hi,

In future, please send your help requests to the GenePattern help forum, https://groups.google.com/u/1/g/genepattern-help, as this email address is no longer monitored regularly.

That said, it seems that job 588894 has already been deleted from the server so I cannot see your input file to provide guidance.  If you are still having trouble please post a new message to the GenePattern help forum (https://groups.google.com/u/1/g/genepattern-help) including the stderr.txt contents and the cls file contents.

Thanks

Ted

On Wed, Jun 26, 2024 at 8:25 PM đông lê <nguoic...@gmail.com> wrote:

Here is the report from stderr.txt
Error in GP.deseq2(gct, cls, confounding.var.cls, opts$qc.plot.format,  :
  The cls.file must be categorical with exactly two classes
Execution halted

So I guess that my cls file has problem.

Vào lúc 10:39:05 UTC+8 ngày Thứ Năm, 27 tháng 6, 2024, đông lê đã viết:

Dear all,

I am new to the group, so perhaps my question could be answered elsewhere, but I can not find the similar topic currently.

Here, I would like to run DEseq2 analysis using my Raw readcount, but the running got error. Please help me with this, since I already check the format of my input .gtc and .cls file and they are all in the correct format.

here is my job ID: 588894. DESeq2

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Ted Liefeld                                      UC San Diego

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