[BioC] Microarray image files in PDF files

[Kevin Coombes]

We have sample QC templates for Affymetrix (and a rough draft for 
Illumina) at
    http://bioinformatics.mdanderson.org/RATb/
Just click on the "startTemplate.cgi" link.

    Keiv

James W. MacDonald wrote:
> 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 
>>> ********************************************************** 
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>