[BioC] select top genes based on p-value in limma
p hu
huut2003 at yahoo.ca
Thu Mar 4 01:01:35 MET 2004
Hi all,
For example, I used
clas<-classifyTests(fit,p.value=0.05)
mycount<-vennCounts(clas, include="both")
and found there are 99 differentially expressed genes for my first comparsion.
then I do:
toptable1<-topTable(fit,coef=1,number=99,genelist=genelist,adjust="fdr")
this is part of the results
Name M t P.Value B
6820 H25306 2.9578622 21.779101 6.712472e-22 39.07274570
6222 H25611 3.8097340 20.616434 3.472310e-21 37.73887184
4394 H12333 2.9868665 13.285336 1.033728e-13 25.92910739
2269 R31747 3.9112632 12.339976 1.164282e-12 23.86703473
9171 R31507 3.7780976 11.834938 4.149866e-12 22.70578573
11306 AA043477 1.6451826 9.087753 2.067361e-08 15.64724863
596 H83378 1.1806774 7.498940 3.972530e-06 11.03899927
9544 H42051 1.5306360 7.202912 9.726446e-06 10.14827317
11320 AA054300 0.9058530 6.899348 2.492575e-05 9.22757718
10132 AA135957 0.8268765 6.552645 7.535515e-05 8.16932543
17941 AA149043 1.2592684 6.404648 1.149187e-04 7.71612881
13461 AA211825 0.7310730 6.082586 3.242677e-04 6.72862309
............................................................
16930 W32999 -0.3562904 -2.861632 3.849730e-01 -2.36371124
17667 W67427 0.4080262 2.859229 3.862250e-01 -2.36921005
7769 H53894 -0.3463782 -2.856329 3.879989e-01 -2.37584026
9751 W92088 -0.3139404 -2.854464 3.887059e-01 -2.38010239
5067 H57545 0.8197179 2.851609 3.902150e-01 -2.38662381
9468 R27989 0.3628438 2.848099 3.902150e-01 -2.39463557
As I can see here, the last gene has very high p-value although it is called DE gene.
So I am wondering how I can select genes based on a cut off p-value rather than a number that indicates how many genes I want to pick???
Thanks
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