[BioC] Microarray image files in PDF files

Thu Apr 15 09:27:59 CEST 2010

Hi all,

Thanks for your help. So I will try to get a grip on Sweave and Latex. The alternativ Sweave sounds pretty good, but gives an error message, when I try to source it (error message and sessionInfo below). I will get back to you if I manage to make the pdfs.

Kind regards,

Mike

> source("Sweave.R")
Error in source("Sweave.R") : Sweave.R:2:1: unexpected $end

> sessionInfo()
R version 2.10.0 (2009-10-26) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
[1] utils     stats     graphics  grDevices datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.10.0

-----Ursprüngliche Nachricht-----
Von: "James W. MacDonald" <jmacdon at med.umich.edu>
Gesendet: 13.04.2010 17:22:32
An: Mike Walter <michael_walter at email.de>
Betreff: Re: [BioC] Microarray image files in PDF files

>Hi Mike,
>
>Mike Walter wrote:
>> 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.
>
>Yep. I thought you were doing something like that. At one time I worked 
>in a core lab as well, and I used Sweave to create all the reports I 
>gave to my clients.
>
>The downside of using Sweave is that you have to learn LaTeX markup as 
>well, but you end up with one document that contains all the verbiage 
>that you give to your clients as well as the code to create the plots 
>and do all the analysis.
>
>All of the BioC packages contain at least one vignette that is based on 
>Sweave, so you can look in the /doc directory for anything with a .Rnw 
>extension for an example. The affycoretools.Rnw file in my affycoretools 
>package is an example of something similar to what I gave my clients.
>
>One slight problem with using Sweave is that the default for all plots 
>is to use a pdf, which doesn't help your situation. There are more 
>elegant ways to get around this obstacle, but I use the klugetastic 
>method of creating the png file and then inserting it manually. As an 
>example (which won't likely make sense just yet):
>
><<echo=false, results=hide>>=
>png("thefile.png")
>image(qc.PLM, which=1, add.legend=TRUE, <otherargs>)
>dev.off()
>@
>
>\begin{figure}[htbp]
>\centering
>\includegraphics{thefile}
>\caption{An image}
>\end{figure}
>
>The first part creates the image invisibly (tin the output file) and the 
>second part puts it in the document. If you have multiple images, you 
>can put them up four at a time using layout(matrix(1:4, ncol = 2, byrow 
>= TRUE)) to save space.
>
>The various vignettes are an excellent resource to get started, and the 
>main Sweave documentation can be found at:
>
>http://www.stat.uni-muenchen.de/~leisch/Sweave/
>
>Best,
>
>Jim
>
>
>> 
>> 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
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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 734-615-7826 
>>> ********************************************************** 
>>> Electronic Mail is not secure, may not be read every day, and
>>> should not be used for urgent or sensitive issues
>
>-- 
>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
>734-615-7826
>**********************************************************
>Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues