[BioC] Remove some genes from analysis in limma package? Is it possible?

James Wettenhall wettenhall at wehi.edu.au
Fri Oct 24 06:45:45 MEST 2003


RG and MA objects in limma are subsettable, so you can select 
the genes you want, e.g.

MAnocontrols <- MA[RG$genes[,"ID"]!="control",]

or you might want to define a "status" vector, as used in the 
plotMA function:

status <- rep("gene",nrow(RG$genes))
status[grep("control",RG$genes[,"ID"])] <- "control"
MAnocontrols2 <- MA[status!="control",]

The "grep" method allows you to select multiple spots and give 
them the same spot type status, e.g. Calibration_Control_1 and
Calibration_Control_2 could all be given the spot type 
"calibration" and then excluded from the analysis.

You could replace "control" above by "ZZZZXXX21".

Hope this helps,

James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall at wehi.edu.au
 of Medical Research,                     Mobile: (+61 / 0 ) 438 527 921    
1G Royal Parade,
Parkville, Vic 3050, Australia

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