Hi Everybody, I am facing problem in understanding the reason for difference among samples when sorted on basis of T-stats. When same samples are sorted on Fold Change than they show consensus in top genes. There are total of 7 samples (Illumina microarray), 5 (P8,P12,P20,P42,P52) from one study and two (P0 and P30) from other two studies. So, 7 samples from 3 studies and one control. I performed standard micro-array analysis, imported samples ( 7 samples) from separate files (3 files), performed normalization, combined using 'lumi' package, filtered out absent probes, reduced probes to gene level and used 'limma' to perform decideTests. As usual, I ranked genes on basis of T-stats. While sorting genes on basis of these ranks I found that if sorted on any of two columns (P0 and P30) there is a clear pattern of matching ranks between these two columns but totally different from other 5 columns. So, these 2 columns show consensus in ranks and other 5 columns show consensus in rank. Please see attached result snippet. But when sorted by Fold change of any sample, all the samples show consensus by showing same top genes. It does not matter which sample is used for fold change based sorting the genes are (almost) same i.e consensus among samples. If you see that attached file which is sorted on fold change, you will notice a pattern in Ranks (Column C-G) among samples i.e. sample P0 and P30 showing similar ranks whereas all other showing different ranks. So, my question is why samples when ranked with t-stats are not showing consensus where as when ranked with Fold Change shows consensus in top genes. Is it a batch effect? I would really appreciate your help in understanding the problem. AK