[BioC] Limma: setting expression values to NA

[James MacDonald]

How about something like this?

index <- RG$genes[,"Status"]!="Gene"
RG$R[index,] <- NA
RG$G[index,] <- NA

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Edo Plantinga" <A.E.D.Plantinga at med.rug.nl> 01/28/04 04:21AM >>>
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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