[BioC] Microarray image files in PDF files

[Benilton Carvalho]

Thibaut Jombard is the best person to contact about this. b

On Thu, Apr 15, 2010 at 8:27 AM, Mike Walter <michael_walter at email.de> wrote:
> 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
>>>>> mailing list Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>>>>> archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>> -- 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
>