[BioC] Saving all AffyPLM residual plots to disk

[James W. MacDonald]

Hi Leif,

Here is some code I use to do this. Here I assume you have both an 
ExpressionSet called 'eset' and a PLMset called 'plm'. I usually use 
oligo, so in my case it is an oligoPLM object, but no matter.

sn <- gsub("\\.CEL", "", sampleNames(eset))
## don't re-make existing plots
if(!all(file.exists(paste(sn[length(sn)], "png", sep = ".")))) {
    sn <- sn[!file.exists(paste(sn[length(sn)], "png", sep = "."))]
    for(i in seq_len(length(sn))){
        png(paste0(sn[i], "png"))
        image(plm, type = "residuals", which = i)
        dev.off()
    }
}


Best,

Jim


On Tuesday, October 01, 2013 1:43:37 PM, Peterson, Leif wrote:
> We are interested in saving all the AffyPLM residual plots to disk (in a single folder) but cannot find syntax in the user's guide or in forums on how to do this.   Thx ahead of time, LP
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099