[BioC] Limma: setting expression values to NA

[Sean Davis]

If you have a RG list, subsetting in limma is pretty easy, I think.  See
help(subsetting) with limma loaded.  To get the subset of your RG list
without Control spots, just do (untested):

RGnocontrol <- RG[RG$genes[,"Status"]!="Gene",]

Sean

----- Original Message -----
From: "Edo Plantinga" <A.E.D.Plantinga at med.rug.nl>
To: "Bioconductor" <bioconductor at stat.math.ethz.ch>
Cc: <stephen at iwinet.rug.nl>; "Rudi Alberts" <R.Alberts at cs.rug.nl>
Sent: Wednesday, January 28, 2004 4:21 AM
Subject: [BioC] Limma: setting expression values to NA


> 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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>
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