[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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