Hi, I did my analysis on GeneChip Mouse Gene ST 2.0 Array, Affymetrix. I compared expression profiles of 4 experimental groups and got some dissapointig and surprising results). At best 2 genes are differentially expressed (limma, adjusted p 0.05 - BH correction) between groups, and none at all between some. Biologically, it doesnt make much sense to get no difference (we are comparing inflammatory cells in joints of arthritic mice and control mice that dont have arthritis), but I guess the changes are not necesarily on transcription level. Now I find myself with all those microarrays and expression values, but the pipeline for analysis sort of stops here since for further pathway/functional analyses are all based on experimental group comparison. Is there a way to find out anything about this cells that we analyzed in general - not in the sense of between group comparison? Like are they activated inflammatory cells or not or something form the expression values? Is it possible to do some enrichement for gene sets that have high expression values even though they are not different between groups? Is it possible to compare the values within one array (gene of interest - housekeeping gene)? From what I know about microarrays, the analysis is based on comparison of experimental groups and expression values by istelf dont mean anything at all, so I realize this questions probably dont make sense but I wanted to double check if there is some way to put this enormous set of expression data into good use.