Hi Jing. See below.
On 17/03/2009, at 2:54 AM, jing wrote: > To whom it may concern, > > I'm analyzing some Affy human exon array data and hope to generate > similar plots as seen in the supplementary figures in the Purdom 2008 > Bioinformatics paper. To do so, I need to get the normalized probe > intensities and residuals. > > I've already followed the steps described in the Human Exon Array > Analysis vignette and get the following: > > (1) ... > csN <- process(qn, verbose=verbose) > > (2) ... > res<-getResidualSet(plmTr) > > I tried the function "extractDataFrame(...,addNames=TRUE)" hoping to > get the data plus column labels for my samples but it didn't work. Is > there any easy way to extract these two sets of data in matrix format > similar to the FIRMA score matrix with probe ID and column labels? Thats right. extractDataFrame() is typically used for some kind of summarized data. For example, you can use extractDataFrame() for pulling out FIRMA scores (summarized at the probeset level), or RMA summarized data (summarized at probeset or gene level). To pull out the raw/normalized data and the residuals, you can use extractMatrix() or readUnits(). I prefer the former. Probably its best to suggest you look at the thread: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/46d609076d9580fb Look for the commands after the "# starting from PLM ..." line. I've been meaning to put up a page giving a summary of these commands, including how to use exon array data with GenomeGraphs. Hopefully I can find some time shortly to do that. Hope that helps. Mark > Thanks, > > Jing > > Jing Ma > Hartwell Center for Bioinformatics & Biotechnology > St. Jude Children's Research Hospital > > > ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
