Hi All, I do Gene Set Enrichment Analysis to two data set from GEO of the same disease. I find that enriched gene sets of two data set have an overlap at only about 60%. I am a new guy to analyze Microarray data. Is this a reasonable results? What are the potential reasons of these differences, since two data set are for the same disease? Thanks. Feng [[alternative HTML version deleted]]

On Thu, Mar 14, 2013 at 10:56 AM, Feng Tian <fengtian@bu.edu> wrote: > Hi All, > > I do Gene Set Enrichment Analysis to two data set from GEO of the same > disease. I find that enriched gene sets of two data set have an overlap at > only about 60%. I am a new guy to analyze Microarray data. Is this a > reasonable results? What are the potential reasons of these differences, > since two data set are for the same disease? > Hi, Feng. This sounds reasonable, yes. There are many potential differences including biological variability, technical variability, disease heterogeneity, and platform differences, to name a few. Sean [[alternative HTML version deleted]]