[BioC] Subsetting limma TestResults

Michael Strehle mstrehle at mdc-berlin.de
Thu Jun 8 14:47:09 CEST 2006

Dear all,

I recently encountered a problem subsetting limma TestResults on a  
new Bioconductor install. If I do

 > results<-decideTests(fit3,adjust="holm")
 > results[results<0]

to extract differentially expressed genes from a MOE4302 fit I will  
get a matrix with results and Affy ID

 > results[results<0]
   1427262_at   1427263_at 1436717_x_at ...
           -1           -1           -1 ...

in R 2.1.1, limma 2.0.8 on OSX 10.4.6/PPC, but

 > results[results<0]
   [1] -1 -1 -1 -1 -1 -1 -1 -1 -1 ...

in R 2.3.0, limma 2.7.3 on OSX 10.4.6/PPC, that is, the results  
without Affy ID .

Same if I use subset(results, results<0). Since I really would like  
to retain the Affy IDs in the subset for further annotation - am I  
missing something here, and is there a way to make this work again ?



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