[BioC] All equal high p-values from limma topTable . What to do ? Need help...
Giulio Di Giovanni
perimessaggini at hotmail.com
Thu Mar 23 17:14:23 CET 2006
Hi I'm looking at the results of an analysis on 4 S. Cerevisiae cDNA arrays,
(2 of these have a dye-swap).
I followed the example in limma user's guide (that if I'm not wrong is
exactly my case).
I obtain a topTable of genes of this type
Block Row Column ID Name M A t P.Value B
4030 30 11 11 YLR162W :::::1: 1.624122241 6.560234285 4.467743568 0.997257765 -2.0502737
1254 10 4 11 YDR166C SEC5:::::1: -0.56584704 5.143049435 -3.824556839 0.997257765 -2.61592631
1113 9 4 1 YDR409W :::::1: 1.016356426 4.282139218 3.988554403 0.997257765 -2.683464218
2115 16 10 5 YKL209C STE6:::::1: -0.540528098 7.340027942 -3.533312325 0.997257765 -2.686586054
5022 37 16 11 YPR070W :::::1: -0.493446684 6.765075537 -3.415141086 0.997257765 -2.77744221
3642 27 14 3 YOL045W :::::1: -0.678996258 5.185557216 -3.448815561 0.997257765 -2.865258763
1602 12 14 3 YNL253W :::::1: -0.542907069 6.019893924 -3.427152231 0.997257765 -2.880360788
4177 31 13 1 YNL221C POP1:::::1: -0.49777162 6.787712846 -3.274291885 0.997257765 -2.8886384
Where all the p-values are 0.997257765. I read in the topTable help that
"if there is no good evidence for differential
expression in the experiment, that it is quite possible for all
the adjusted p-values to be large, even for all of them to be
equal to one."
I'm quite astonished ... and now ?
This fact implies that is not a good experiment ? Or that data were not well
preprocessed ? Or maybe that for that experiment there are no genes
significantly differently expressed ?
I'm analyzing that data from a Biomolecular lab, and I don't know what to do
and how to explain this...
I'll be very happy for any help or suggestion ... !!!!!
Thanks in advance,
Giulio...
This
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