Updating to the latest version of R and limma got rid of the error. Thanks for the reply. John ----- Original Message ----- From: "Herve Pages" <hpages@fhcrc.org> To: "John Fernandes" <jfernand at="" stanford.edu=""> Cc: "bioconduct" <bioconductor at="" stat.math.ethz.ch=""> Sent: Friday, June 15, 2007 12:40 PM Subject: Re: [BioC] warning (condition has length>1) when reading in Agilent hyb text files Hi John, limma 2.9.17 is old and this problem seems to have been fixed in more recent versions of limma: hpages at lamb1:~/svn/Rpacks-2.1/limma/R> svn log -v -r 24408 -------------------------------------------------------------------- ---- r24408 | smyth at wehi.edu.au | 2007-04-30 21:17:31 -0700 (Mon, 30 Apr 2007) | 5 lines Changed paths: M /trunk/madman/Rpacks/limma/DESCRIPTION M /trunk/madman/Rpacks/limma/R/read-maimages.R M /trunk/madman/Rpacks/limma/inst/doc/changelog.txt 1 May 2007: limma 2.11.1 - Bug fix to read.columns() to stop spurious warning message when text.to.search has length greater than one. -------------------------------------------------------------------- ---- I recommend you update your limma package. Also you could update to R 2.5.0 and Bioconductor 2.0: many things have changed between BioC 1.9 and BioC 2.0 and a lot of bugs have been fixed ;-) Cheers, H. John Fernandes wrote: > Anyone have an idea what could be causing the warning I'm getting? Do > you need more info from me? Can I look up the error somewhere? > > Thanks, > John > > >> 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 & >> x[,"gIsFeatNonUnifOL"]==0 >> as.numeric(okAboveBG & okSaturated & okPopnOutlier & >> okNonUnifOutlier) >> } >> >> RG <- read.maimages(targets$FileName,path=hybpath,source="agilent", >> >> columns=list(Rf="rMedianSignal",Gf="gMedianSignal",Rb="rBGMedianSig nal",Gb="gBGMedianSignal"), >> other.columns=othercols,wt.fun=myfunFE) >> >> 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. >> >> Thanks, >> John Fernandes >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor