[BioC] No consensus among samples when sorted with t-stats - Need Help

[Atul Kakrana]

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