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count data from microarray dataset 72 CEL file and related ARR files.
hi everyone, I am new about MicroArray datasset, so want to ask how can i generate the count data from microarray dataset 72 CEL file and related ARR files. will appreciate your help.
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Microarrays work with intensity values, not counts. The CEL files are the raw data generated by Affymetrix arrays, they can be processed e.g. with the oligo package. First load them into R with oligo::read.celfiles and then oligo::rma for normalization and background subtraction. This should give you normalized data on the log2 scale which are ready for processing e.g. differential analysis using the limma package.
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ejem, microarrays don't have count-data, it is based on probe signals. You are mentioning CEL files, so I guess you have Affymetrix data, check R:affy and R:limma for the analysis.
Thank you very much for your reply.