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

[John Fernandes]

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="rBGMedianSignal",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
>