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Forum: Bioinformatics 07-17-2014, 11:13 AM
Replies: 92
Views: 38,162
Posted By crazyhottommy
I did try using all the genes, but still no...

I did try using all the genes, but still no pathways are selected....Maybe that's just the nature of my data?
Forum: Bioinformatics 07-16-2014, 09:27 AM
Replies: 92
Views: 38,162
Posted By crazyhottommy
Thank you very much for your reply. I will feed...

Thank you very much for your reply. I will feed all the genes to GAGE to see, but one question is that the fold change for each gene has different p values (and adjust p values), so GAGE only takes...
Forum: Bioinformatics 07-15-2014, 06:48 PM
Replies: 92
Views: 38,162
Posted By crazyhottommy
Also, if I do want to convert gene set ID from...

Also, if I do want to convert gene set ID from Entrez to symbol.
How can I do it?

Thank you.
Forum: Bioinformatics 07-15-2014, 06:46 PM
Replies: 92
Views: 38,162
Posted By crazyhottommy
Thank you, I followed it, after DESeq. 1724...

Thank you, I followed it, after DESeq. 1724 differentially expressed genes were used for pathway analysis.

res <- nbinomTest( cds, 'control, 'treat' )

resSig <- res[ res$padj < 0.01 &...
Forum: Bioinformatics 07-14-2014, 12:56 PM
Replies: 92
Views: 38,162
Posted By crazyhottommy
Hi there, thank you for making this awesome tool....

Hi there, thank you for making this awesome tool.

I am working with mouse data, I want to know how to convert the gene set into gene symbol format.

kg.mouse<- kegg.gsets("mouse")
kegg.gs<-...
Forum: Bioinformatics 11-17-2013, 07:35 PM
Replies: 92
Views: 38,162
Posted By crazyhottommy
Thank you!

Thank you!
Forum: Bioinformatics 11-15-2013, 01:36 PM
Replies: 92
Views: 38,162
Posted By crazyhottommy
Hi I was playing around with GAGE, one question...

Hi I was playing around with GAGE, one question is that I got the count table by HTSeq, and the ids are gene names for each row, how can I change the gene names to GO term ids?

Thanks
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