R.2.14 in RStudio all packages up to date.

Using the contrast.matrix I have been using lmfit etc from Limma, and have obtained a very informative Venn Diagram of our results (all trts minus healthy)...  I would like to find the top 25 (in one trt only 5 genes were unique to the pathogen)  up and down regulated genes... for each pathogen vs Healthy contrast. The code below gives me total across all the contrasts, or appears to.   Have googled and read most of day but  have found no code etc for doing this, or do I need to make a matrix for each comparison separately?     I tried topTableF in the tops code (given topTableF provided the contrast data) but result was NA's...

> design  #each trt 4 CEL file replicates no subtreatments
   Virus Bacteria Healthy phytoplasma
1    0        1       0     0
2    0        1       0     0
3    0        1       0     0
4    0        1       0     0
5    1        0       0     0
6    1        0       0     0
7    1        0       0     0
8    1        0       0     0
9    0        0       1     0
10   0        0       1     0
11   0        0       1     0
12   0        0       1     0
13   0        0       0     1
14   0        0       0     1
15   0        0       0     1
16   0        0       0     1


fit <- lmFit(eset, design)
contrast.matrix<-makeContrasts(Bacteria-Healthy, Phytoplasma-Healthy, Virus-Healthy, levels=design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
topTable(fit2, adjust="BH", n=20)
results<-decideTests(fit2)
vennDiagram(results)
topTableF(fit2, n=20)

tops <- topTable(fit2, n=Inf) # all on chip
tops[which(tops$logFC > 0), ] [1:25,] # up reg top 25
tops[which(tops$logFC < 0), ] [1:25,] # down reg top 25

thank you in advance for all help....

Whether you think you can or think you can't - Your're right...
Henry Ford

Cristina Paul






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