[BioC] Limma: setting expression values to NA

[Edo Plantinga]

Dear all,

I would like to do a principal components analysis of a microarray experiment. In order to do this, I first need to set the expression values of my control spots to NA, so that this analysis is not influenced by these spots. The problem is that I do not know how to achieve this.
I can list my control spots by:
RG[RG$genes [, "Status"] != "Gene",]
I would like to set the corresponding RG$R and RG$G expression values to NA. I can set them to zero by:
RG$R <- RG$R * (RG$genes [, "Status"] == "Gene")
but this is not what I want. If I try:
RG$R <- RG$R * (if(RG$genes [, "Status"] == "Gene") {NA} else {1})
I get the warning message: 
the condition has length > 1 and only the first element will be used in: if (RG$genes[, "Status"] == "Gene") { 
Can anybody help me out?

Kind regards,

Edo Plantinga

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