difficulty with opening Affymetrix cel files

Question

[hosseinkhan]

Hi

I am trying to work with affymetrix cel files, but when I try to extract cel files most of them are opened in a text file with modified and unreadable format.

I appreciate any help in advance

Answer 1

[poisonAlien]

Hi,

I am not sure when you say extract the cel files, but CEL files cannot be opened in a text editor. You need a particular software for reading them. You can extract the raw intensities from CEL files in R using affy bioconductor package using readAffy() function.

[hosseinkhan]

Hi, thanks for replying to my question. Yes I know that I have to use ReadAffy() function in R, but when I want to import my cel files in a program(AnyExpress) to combine them, I get a error. So I tried to open my cel files to see if there is some thing wrong with their contents. Some of them are opened in text file perfectly but most of them are unreadable. Anyway thank you again

PhD candidate of Bioinformatics, Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran

[David Westergaard]

cel files are per definition binary files, so they are not human readable in any way. Instead of using AnyExpress, I would suggest you try the same procedure using the R/Bioconductor package affy, as suggested. The cel files may be corrupt, but that is nearly impossible to see by just opening them in a text-editor.