[BioC] (no subject)

[Eliana Lucchinetti Zaugg]

Hello!
I have a question concerning data interpretation in LIMMA. First of all I'll give you the commands:

contrast.matrix<-makeContrasts(APC-ISCH,IPC-ISCH,levels=design)
fitPRECOND2<-contrasts.fit(fit,contrast.matrix)
fitPRECOND2<-eBayes(fitPRECOND2)
clas3<-classifyTestsP(fitPRECOND2,p.value=0.01,method="fdr")
vennDiagram(clas3,include="up")
vennDiagram(clas3,include="down")

So far, no problem! I've got nice Venn diagrams. After that my input was:

topTable(fitPRECOND2,number=20,genelist=NULL,coef=1,adjust="fdr")

which yielded:

              M         t    P.Value         B
2380 -1.0241489 -6.058845 0.01147946 5.0373154
379  -0.8440311 -5.464009 0.02976549 3.6259203
2382 -0.9576517 -5.261334 0.02976549 3.1387221
8436 -0.6746846 -5.216491 0.02976549 3.0306287
2383 -0.7343412 -5.064616 0.03638846 2.6639293
7974 -1.0281853 -4.889561 0.04943332 2.2404780
7925 -0.8519961 -4.833610 0.04952967 2.1050515
2384 -0.7728411 -4.698536 0.05865728 1.7781412
432   0.5732701  4.656867 0.05865728 1.6773365
7680  0.5717780  4.640318 0.05865728 1.6373117
7927 -0.7303740 -4.598890 0.05865728 1.5371476
2569  0.5033168  4.579322 0.05865728 1.4898512
1688  0.6904956  4.540636 0.06028835 1.3963860
6603  0.5590289  4.506030 0.06162635 1.3128274
5487 -0.7299432 -4.425216 0.07196002 1.1179075
3247  0.6442329  4.377510 0.07698329 1.0030059
5501 -0.8589314 -4.348990 0.07839810 0.9343814
7434  0.7573137  4.293568 0.07860314 0.8011835
7230  0.6309675  4.277457 0.07860314 0.7625059
8527 -0.8768646 -4.252795 0.07860314 0.7033388

It occurred to me that none of the p-palues in the ranking was below p=0.01. Why were there significantly differentially regulated genes in my Venn diagrams (constructed using p=0.01)?

Second question:
Do the numbers in the first column correspont to the row number in the eset (expression set, I used RMA to do the analysis)?

THANKS IN ADVANCE!
ELIANA

===============================
Eliana Lucchinetti Zaugg, PhD
Institute of Pharmacology and Toxicology 
Section of Cardiovascular Research-Room 17 J 28
University of Zurich
Winterthurerstr. 190
CH-8057 Zürich (Switzerland)
 
Phone: +41-1-635 59 18
Fax: +41-1-635 68 71
e-mail: eliana.zaugg at pharma.unizh.ch


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