Hi, I'm working on some Affy mice chips, they are Mu11KsubA and Mu11KsubB. The data on the chips are divided into two parts (maybe the gene list is long), so when I try to read the data to R, it gave me an error message saying "Error in initialize (value,....) : Cel file C:/~/1DE_Mu11KB.CEL does not seem to be of Mu11KsubA type.   Is there a way I can combine the data into one, instead of analyzing two parts separately? Thanks. Yen Lin

Hi, Yen Lin: The error message is caused by the non-matching CDF/CEL file (A/B array). There is a logical reason to keep them separately analyzed. The major argument is the hybridization condition and thus normalization considerations. After normalization and RMA gene indexing, please feel free to combine them. I also tried to use unigene ID, instead of AffyID to combine the A/B array. It works. Simon ================================================= Simon M. Lin, M.D. Manager, Duke Bioinformatics Shared Resource Assistant Research Professor, Biostatistics and Bioinformatics Box 3958, Duke University Medical Center Durham, NC 27710 Ph: (919) 681-9646 FAX: (919) 681-8028 Lin00025 (at) mc.duke.edu http://dbsr.duke.edu ================================================= Subject: [BioC] Mu11KsubA and Mu11KsubB To: bioconductor@stat.math.ethz.ch Message-ID: <400F6440.36761406@stanford.edu> Content-Type: text/plain; charset=x-user-defined Hi, I'm working on some Affy mice chips, they are Mu11KsubA and Mu11KsubB. The data on the chips are divided into two parts (maybe the gene list is long), so when I try to read the data to R, it gave me an error message saying "Error in initialize (value,....) : Cel file C:/~/1DE_Mu11KB.CEL does not seem to be of Mu11KsubA type. Is there a way I can combine the data into one, instead of analyzing two parts separately? Thanks. Yen Lin