[BioC] Microarray image files in PDF files

[Mike Walter]

Hi Jim, 

We are a core lab. So I'd like to generate a QC report for our customers with all kind of plots to judge the quality of the data. This includes e.g. density plots, boxplots before and after normalization, RNA degradation plots, PCA, MAS5 scaling factor, rel log expression etc. All these plots are quite small and you can easily just make a script that produces the pdf. However, when I use for example

library(affyPLM)
data = ReadAffy(celfile.path=celfile, filenames=filenames)
qcPLM = fitPLM(data)
pdf("QC_report.pdf", paper="a4", version="1.4")
for (i in 1:length(data)){
image(qc.PLM, which=i, add.legend=TRUE, main=paste(sampleNames(data)[i], "weights", sep=" - "))
}
dev.off()

Then the pdf files become quite large. Of course, I can use png() or savepng() instead of pdf(), but then the files are not in my pdf file and I have to generate a pdf from the images manually and attach it to the QC report. Thus my question was: Can I generate a low resolution image that is then put forward to the pdf device. I already played a little bit with dev.print() and dev.copy() functions but had no real clue how to make it.

I hope this makes my question a little bit clearer.

Thanks for your help and kind regards,

Mike





-----Ursprüngliche Nachricht-----
Von: "James W. MacDonald" <jmacdon at med.umich.edu>
Gesendet: 13.04.2010 15:27:32
An: Mike Walter <michael_walter at email.de>
Betreff: Re: [BioC] Microarray image files in PDF files

>Hi Mike,
>
>Mike Walter wrote:
>> Hi all,
>> 
>> 
>> 
>> I'm looking at images of Affy arrays for QC using images(Affybatch)
>> or images(affyPLMObject). However, when I include this images in PDF
>> files these tend to get incredibly large. Therefore, my question
>> would be, is there a method to generate a png or jpg image and
>> include this in the pdf file?
>
>The simple answer is yes. See ?png. But somehow I think the question is 
>more involved than that. Rather than speculating as to what you want, do 
>you have a more directed question with perhaps an example?
>
>Best,
>
>Jim
>
>
>> 
>> 
>> 
>> Any hints are highly appreciated,
>> 
>> 
>> 
>> Kind regards,
>> 
>> 
>> 
>> Mike
>> 
>> _______________________________________________ Bioconductor mailing
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>
>-- 
>James W. MacDonald, M.S.
>Biostatistician
>Douglas Lab
>University of Michigan
>Department of Human Genetics
>5912 Buhl
>1241 E. Catherine St.
>Ann Arbor MI 48109-5618
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