[BioC] reading binary .CEL files in MACOSX

Martino Barenco sejjmba at ucl.ac.uk
Wed Apr 15 14:52:21 CEST 2009

Dear list,

Within the affy package and on a MACOSX machine (10.4.11), I want to  
access probe-level data on binary .CEL files (human st1 expression  
arrays) using the command ReadAffy, which creates an "AffyBatch"  
object. I get the following meassage:

Error in read.affybatch(filenames = l$filenames, phenoData = l 
$phenoData,  :
	Is NT_BAY.CEL really a CEL file? tried reading as text, gzipped  
text, binary and gzipped binary.

I suspect it is a problem with the .CEL files themselves, as I don't  
get this on a window machine when I attempt to read the very same  
file. Also when I attempt to read text .CEL files, on the same MACOSX  
machine, I don't get that message either.

- Is there anything I should do to modifiy those binary .CEL files to  
make them readable on the MAC? (chage the carriage returns for example?)
- Or a way to turn a binary .CEL file into a text one?

In advance, many thanks.


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