[BioC] Limma error - undefined columns selected

[Gordon Smyth]

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