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 > > > > -----Urspr?ngliche 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 >>> >>> >>> >>> >>> >>> -----Urspr?ngliche 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 >