File formatting issues

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Toni Delorey

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Jul 18, 2013, 5:16:10 PM7/18/13
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Hello,

I have pvalues for differentially expressed genes in two yeast samples,under different conditions. I'm trying to find the pathways that are significantly associated to (up and down regulated) genes within and between samples. All of the examples and tutorials that I can find that I believe might apply to this analysis start with .cdm files. I only have excel files. When I try to import them, Gitools calls it a .tdm file. I think this is one of the reasons the heat maps I'm getting are not making sense.

Any insight? I've attached the files that I'm trying to work with.

Thanks!
Toni
inputdata.xlsx
saccharomyces_cerevisiae__kegg_pathway__ensembl_sgd_gene_annotations.tsv
saccharomyces_cerevisiae__kegg_pathway__ensembl_sgd_gene.tcm

Christian Perez-Llamas

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Jul 19, 2013, 3:44:58 AM7/19/13
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Hello,

I think it is not working because Gitools expect the Excel file to be like in the TDM format but your Excel is like in the CDM format.

You have this:



and it should be like this:



I don't know of any Excel macro that could transform the data in this way.

Hope this helps you.



Toni

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Christian Perez-Llamas
Biomedical Genomics Group
Research Unit on Biomedical Informatics (GRIB)
Pompeu Fabra University @ PRBB

http://bg.upf.edu
http://www.intogen.org
http://www.gitools.org

Christian Perez-Llamas

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Jul 19, 2013, 3:47:00 AM7/19/13
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I pasted two images but seems that googlegroups doesn't like that.

You have this:

id SCER_t60 SCER_t31
YAL001C 0,096804768 0,6703410618
YAL002W 0,203744596 0,6604577814

and should be like this:

row column value
YAL001C SCER_t60 0,096804768
YAL001C SCER_t31 0,6703410618
YAL002W SCER_t60 0,203744596
YAL002W SCER_t31 0,6604577814

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