Hi all,

I have samples from several individuals from two different time points (e.g., individual 1 day 1, individual 1 day 30, individual 2 day 1, individual 2 day 30, etc.). Each individual has two samples, one at each time point. I have already looked at differential expression of the genes independently of one another, and now I would like to perform GSEA (http://software.broadinstitute.org/gsea/index.jsp) or a similar analysis on my RNA-seq data from these samples to identify groups of genes that are collectively differentially expressed between the two time points (essentially the same goal as the unanswered question found here: Pathway Analysis For Paired Microarray Data & Paired Rna-Seq Data? ). The GSEA faq says it cannot be used directly with paired samples, but that "if you create a ranked list of genes by running a paired-sample marker analysis outside of GSEA, you can use GSEA to analyze that ranked list of genes."

1) Is anyone aware of a documented, robust way to rank genes using paired samples as described above?

2) If not, is there a method similar to GSEA that takes into account a paired design?

Thank you!