Question: limma: get list of genes after classifyTestsF
gravatar for Bandyopadhyay, Somnath Som
11.7 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.

ADD COMMENTlink modified 3.5 years ago by Gordon Smyth35k • written 11.7 years ago by Bandyopadhyay, Somnath Som60
gravatar for Gordon Smyth
3.5 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)

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)
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Gordon Smyth35k
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