Hi Kathy, Assuming the chips are all the same species, I would probably use something like MergeMaid. There may be others -- you can check here: http://bioconductor.org/packages/2.2/DifferentialExpression.html Best, Jim Kathy Duncan wrote: > Hi Jim, > > Thanks ! > > Further, I'm eagerly looking forward to comment(s) on the methods of > integrating those separately processed and analyzed data, as you have > mentioned. > [Else, pointers towards some ref. would also be helpful] > > kathy > > > > > > On Sat, Apr 12, 2008 at 1:38 AM, James MacDonald <jmacdon at="" med.umich.edu=""> <mailto:jmacdon at="" med.umich.edu="">> wrote: > > Hi Kathy, > > The different chip types will have to be processed and analyzed > separately. The easiest way to do so is to make separate > subdirectories and put the different chip types in their own directory. > > Best, > > Jim > > > > Kathy Duncan wrote: > > Hi All, > > I've got an Affymetrix dataset which I need to process and > finally get the > list of genes and their respective expression levels. Without > having much > prior idea and experience, I tried the ReadAffy() function > within the > directory containing the .CEL files and I came across the error > saying : > > Error in read.affybatch(filenames = l$filenames, phenoData = > l$phenoData, : > > Cel file MN.CEL does not seem to have the correct dimensions > > Then I tried the following command for each individual .CEL > files of that > investigation (as I am not sure how to get such information > about all the > files using a single command): > > whatcdf ("filename", compress = getOption("BioC")$affy$compress.cel) > > I could see that the investigation is referring to different CDF > files. > > Could you please inform me how I should proceed ! > > kathy > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto: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, MS > Biostatistician > UMCCC cDNA and Affymetrix Core > University of Michigan > 1500 E Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623