how to use GSEA analysis of RNA-seq expression profile data?
Hello everyone I am studying GSEA analysis and I know how to analyze the array expression profile using GSEA desktop application. But I do not know how to use GSEA analysis of RNA-seq expression profile data which display as read counts? Can I use the VOOM function in limma package to normalize the RNA-seq expression profile data and then do it like the array expression profile data? Any reply is welcome, thanks
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It is fairly well described in the GSEA FAQ: Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data? https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ
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Try GAGE which has a RNAseq-GSEA pipeline.