Question

count data from microarray dataset 72 CEL file and related ARR files.

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3.9 years ago

aarvaBioinfo ▴ 10

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.

microarray affimatrix CEL and ARR files ChIP-Seq R • 2.0k views

ADD COMMENT • link 3.9 years ago by aarvaBioinfo ▴ 10

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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.

ADD REPLY • link 3.9 years ago by JC 13k

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Thank you very much for your reply.

ADD REPLY • link 3.9 years ago by aarvaBioinfo ▴ 10

score 1 · Answer 1 · 2020-05-21

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3.9 years ago

ATpoint 82k

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.