I am pursuing Pathway Analysis for two different analyses. The first is a paired microarray dataset and the second is an RNA-Seq paired dataset.
Many tools available for pathway analysis don't take into consideration paired (matching) data. In the microarray world exist much methodology on how to rank a list of genes (for example WAD and FC methods) then feed this preranked into the tool, if it doesnt already have a tool built in to do the ranking. Is anyone aware of either
A. methodolgy to rank paired data across numerous subjects or B. tools that will incorporate paired data into the analysis.
I am aware GSEA, PathwayExpress, GeneTrail and David will not take matching data into consideration.
Additionally, I am interested to know if there are any pathway analysis tools apart from GO-Seq that is compatible with RNA-Seq data.