Entering edit mode
Dear Atul,
The description of your analysis doesn't make sense to me. How could
you
have t-statistics for individual samples P0 and P30?
If you want help with code, then please give code. See the posting
guide.
The software developers only give advice on using code -- we don't
analyse
or trouble-shoot individual experiments on the list.
Best wishes
Gordon
--------- original message ------------
Atul Kakrana atulkakrana at outlook.com
Thu Jun 6 05:42:15 CEST 2013
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
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