Hi. On Mon, Aug 24, 2009 at 12:21 PM, mbaudis<mbau...@gmail.com> wrote: > > Dear all, > > I have posted a script and associated files to make it easier to: > > 1. process various types of Affymetrix genotyping array batches, using > aroma.affymetrix, but with > > 2. (IMHO) improved value & segmentation plotting options (no EBImage, > PDF output, inclusion of CNV regions, inclusion of >7800 "cancer > related" genes ...)
thanks. This looks great. It is also useful to me to see how others are trying to setup a pipeline. Eventually I hope we'll end up with a fairly standard and user-friendly pipeline. FYI, EBImage is used by aroma.affymetrix for generating spatial images of CEL files; generating PNGs using image() was simply painfully slow. Other than that, standard PNG output is generated for all other cases. > > The comment can be found at > > http://groups.google.com/group/progenetix/web/aroma-affymetrix-processing-visualization > > The method has been used extensively here (e.g. currently for all GEO > Affy genotyping files, up tp >700 x 250k), and seems robust. However, > you have to tune it for your environment. Thanks for sharing this experience (700 arrays). > > I sometimes run into memory leakage problems, but this is probably not > due to the front-end ... > > Pls. feel free to use & modify; however, I would be very glad for > suggestions how to improve the processing. FYI, although only an alpha version, the R.menu package - installed via hbLite("R.menu") - provides the following: > library("R.menu"); > chipTypes <- c("GenomeWideSNP_6", "Mapping250K_Nsp", "Mapping250K_Sty", > "Mapping50K_Hind240", "Mapping50K_Xba240", "Mapping10K_Xba142", > "Mapping10K_Xba131"); > chipType <- textMenu(chipTypes, value=TRUE); 1: GenomeWideSNP_6 2: Mapping250K_Nsp 3: Mapping250K_Sty 4: Mapping50K_Hind240 5: Mapping50K_Xba240 6: Mapping10K_Xba142 7: Mapping10K_Xba131 Selection: 9 Enter an item from the menu. Selection: yadayada Enter an item from the menu. Selection: 1 > chipType [1] "GenomeWideSNP_6" This also allows you do select data set etc from a menu, e.g. path <- Arguments$getReadablePath("rawData/"); dataSets <- list.files(path=path, full.names=TRUE); dataSets <- dataSets[sapply(dataSets, FUN=isDirectory)]; dataSets <- basename(dataSets); arraySet <- textMenu(dataSets, value=TRUE); Also, use byNnn() not fromName(), e.g. AffymetrixCelSet$byName() not AffymetrixCelSet$fromName(). Cheers, Henrik > > Best, > > Michael. > > Dr. Michael Baudis > Institute of Molecular Biology > University of Zurich > Winterthurerstrasse 190 > CH-8057 Zurich > Switzerland > > email michael.bau...@molbio.uzh.ch > web www.molbio.uzh.ch/baudis > > > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
