[BioC] No consensus among samples when sorted with t-stats - Need Help
atulkakrana at outlook.com
Thu Jun 6 05:42:15 CEST 2013
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.
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