Entering edit mode
Dear Ankit,
The error is caused by a bug in the function wtVariables() in limma.
Try sourcing this replacement function into your session and see if
it fixes the problem.
Best wishes
Gordon
wtVariables <- function(x,fun)
# Finds variable names in user-defined functions
# Gordon Smyth
# 3 Nov 2004. Last modified 2 Jan 2006.
{
x <- as.character(x)
a <- deparse(fun)
n <- length(x)
ind <- logical(n)
for (i in 1:n) {
ind[i] <-
as.logical(length(grep(protectMetachar(x[i]),a)))
}
x[ind]
}
At 10:00 PM 28/12/2005, bioconductor-request at stat.math.ethz.ch
wrote:
>Date: Tue, 27 Dec 2005 03:44:20 -0800 (PST)
>From: Ankit Pal <pal_ankit2000 at="" yahoo.com="">
>Subject: [BioC] Limma error - undefined columns selected
>To: bioconductor at stat.math.ethz.ch
>
> Hi All,
> I'm using the latest version of limma to analyse a set of 3 gpr
files.
> The QC filter I have created is as follows
> >myfun <- function(x,threshold=55){
> + okred <- abs(x[,"% > B635+2SD"]) > threshold
> + okgreen <- abs(x[,"% > B532+2SD"]) > threshold
> + okflag <- abs(x[,"Flags"]) > 0
> + okRGN <- abs(x[,"Rgn R2 (635/532)"] ) > 0.6
> + as.numeric(okgreen || okred || okflag || okRGN)
> +}
>
> Onreading in the gpr files using
>
> >RG <- read.maimages(targets$FileName,
source="genepix",wt.fun=myfun)
> I get the following error
>
> Error in "[.data.frame"(x, , "% > B635+2SD") :
> undefined columns selected
>
> I checked the columns and they are present in my gpr file.
>
> Why am I getting this error and how do I go about correcting it
>
> -Ankit