[BioC] Filtering genes based on Agilent flags

[John Fernandes]

I've written one to find spots noted as "well above background":

wtfun <- 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)
}


John


> Hello list,
>
>
>
> I was wondering if anyone knows of a wt.fun function which will filter
> genes based on their flags in an Agilent FE file.  Using the help, I
> have found functions for Spot and GenePix files, but nothing for
> Agilent.  Has anyone had this problem?
>
>
>
> Thanks in advance,
>
>
>
> Wyatt
>
>
>
> K. Wyatt McMahon, Ph.D.
>
> Postdoctoral Research Associate - Functional Genomics Center and
> Services Facility
>
> Texas Tech University
>
> Department of Plant and Soil Sciences
>
> Campus Box 42122
>
> 79409
>
> 806-742-5073 ext. 263
>
>
>
>
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