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Question: limma: get list of genes after classifyTestsF
0
11.8 years ago by

I am using limma to analyze affy data. i made some contrasts and using classifyTestsF(object,p.value=0.01) I get the following results:

  E.OvsC.O I.OvsC.O IM.OvsC.O   E.TvsC.T I.TvsC.T
IM.TvsC.T C.TvsC.O  E.TvsE.O IM.TvsIM.O M.TvsM.O
-1      34     229     798     369     469     430      26     146    1938     820
0   54582   54142   53302   54105   53955   53971   54611   54417   50907   53367
1      59     304     575     201     251     274      38     112    1830     488

Now I wanna make a list of the probests which change in every contrast (increases and decreases separately). how do I make a list of these probesets. Any help would be appreciated and thanks in advance.
Som.

modified 3.7 years ago by Gordon Smyth35k • written 11.8 years ago by Bandyopadhyay, Somnath Som60
1
3.7 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

The output you show is from summary and decideTests:

results <- classifyTestsF(object,p.value=0.01)
summary(decideTests(results))


Suppose you want to see genes that are significantly up for every contrast. The following code will give you a topTable of just those genes:

i <- apply(results>0, 1, all)
topTable(fit[i,], n=Inf)


To see those that are significantly down for every contrast:

i <- apply(results<0, 1, all)
topTable(fit[i,], n=Inf)