Dear Dr Heidi, We are french student in Statistics and we are currently a trainee in a biotechnology company, we are working on microarrays analysis. We want to use your Bioconductor package to analyse microarrays data from Affymetrix on gene expression profile. We want to import data of microarrays from Affymetrix on R, with the package Affy. But we meet the next problem : << affy <- read.affybatch("name_data.CEL") Erreur dans read.affybatch("name_data.CEL") : The affy package is not designed for this array type. Please use either the oligo or xps package. FALSE De plus : Message d'avis : In read.affybatch("name_data.CEL") : Incompatible phenoData object. Created a new one. >> Can you please help us to resolve this problem ? Thank you in advance for your help and your advice. Sincerely, Steven AUGER and Bouchra AFRIAD -- output of sessionInfo(): R version 3.0.0 (2013-04-03) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affy_1.38.1 Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 BiocInstaller_1.10.1 preprocessCore_1.22.0 [4] tools_3.0.0 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

Hi, I think the fix is quite clear, your error message says: On Fri, May 31, 2013 at 10:41 AM, Auger Steven [guest] <guest at="" bioconductor.org=""> wrote: [snip] > But we meet the next problem : > << affy <- read.affybatch("name_data.CEL") > Erreur dans read.affybatch("name_data.CEL") : > > The affy package is not designed for this array type. > Please use either the oligo or xps package. that you should be using a different package to process the data from the arrays you are working, namely the oligo package, or the xps package (these are both bioconductor packages, so you can install them in "the normal way") I guess you are not using the normal/traditional expression arrays (the 3' biased ones) -- maybe you've got exon arrays, or something else? Read through vignettes of the oligo and xps packages to see which one suits you best and go with that one. -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech