[BioC] Saving all AffyPLM residual plots to disk

[Henrik Bengtsson]

On Tue, Oct 1, 2013 at 10:56 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> 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()
>    }
> }

FYI, with the 'R.devices' package the above can be done as:

library("R.devices")
## don't re-make existing plots
options("devEval/args/force"=FALSE)

sn <- gsub("\\.CEL", "", sampleNames(eset))
for(i in seq_along(sn)) {
  toPNG(sn[i], {
    image(plm, type="residuals", which=i)
  })
}

Adjust aspect ratio by specifying argument 'aspectRatio' for toPNG().


A completely different path is to use aroma.affymetrix, e.g.

library("aroma.affymetrix")
csR <- AffymetrixCelSet$byName("GSE9890", chipType="HG-U133_Plus_2")
res <- doRMA(csR, drop=FALSE, verbose=TRUE)
rs <- calculateResidualSet(res$plm, verbose=TRUE)
ae <- ArrayExplorer(rs)
setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow"))
process(ae, interleaved="auto", verbose=TRUE)
display(ae)

That will generate PNGs where each probe on the array occupies exactly
one pixel.  These PNGs can be navigated via the ArrayExplorer.  See
the residual ArrayExplorer example on http://aroma-project.org/demos/
for an example.

/Henrik

>
>
> 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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