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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Differential expression analysis for each patient sample tumor/normal #174

Open rjg2186 opened 6 years ago

rjg2186 commented 6 years ago

Is it possible to perform differential expression analysis for each patient and to get the output logFC for each patient Thanks.

torongs82 commented 6 years ago

Hi @rjg2186 what do you mean for DEA for each patient like single sample ?

DarioS commented 6 years ago

I suppose it's possible to calculate a fold change, but because the comparison involves one sample per condition, you couldn't calculate a meaningful p-value or FDR. Are you requesting GFOLD to be available in TCGAbiolinks?

rjg2186 commented 6 years ago

@DarioS Yes, similar to GFOLD. Thanks