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

[James Wettenhall]

Marcelo,

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

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