[BioC] warning (condition has length>1) when reading in Agilent hyb text files

John Fernandes jfernand at stanford.edu
Thu Jun 14 01:05:20 CEST 2007

I'm reading Agilent text files generated from Feature Extractor 9.5.3 into 
limma with the following:

    myfunFE <- function(x) {
        okAboveBG <- x[,"rIsWellAboveBG"]==1 & x[,"gIsWellAboveBG"]==1
        okSaturated <- x[,"rIsSaturated"]==0 & x[,"gIsSaturated"]==0
        okPopnOutlier <- x[,"rIsFeatPopnOL"]==0 & x[,"gIsFeatPopnOL"]==0
        okNonUnifOutlier <- x[,"rIsFeatNonUnifOL"]==0 & 
        as.numeric(okAboveBG & okSaturated & okPopnOutlier & 

    RG <- read.maimages(targets$FileName,path=hybpath,source="agilent",

I am getting a warning for each file:

    "the condition has length > 1 and only the first element will be used 
in: if (text.to.search != "") for (i in 1:ncn)"

However, I am getting results from the weight function.  Does the warning 
indicate a problem?

I am running R 2.4.1 on Win XP with limma 2.9.17.

John Fernandes

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