[BioC] Help with very old CEL files

[Kasper Daniel Hansen]

On Jun 22, 2007, at 3:24 PM, Jeremy Davis-Turak wrote:

>> Hi Jeremy,
>>
>> Jeremy Davis-Turak wrote:
>>> Hi BioC guys,
>>>
>>> I'm having trouble opening some CEL files from an old project on the
>>> RG_U34A chip.  When I try to use ReadAffy, I get this error:
>>>
>>> Error in read.affybatch(filenames = l$filenames, phenoData = l 
>>> $phenoData,  :
>>>         Is ***01_N1.CEL really a CEL file? tried reading as text,
>>> gzipped text and binary
>>
>> You can also get this error if the file has been corrupted. Do you  
>> get
>> the same result with all of your files, or just this one?
>
> All of the files have this error.

You could try with affxparser. I do not know how the Fusion SDK deals  
with older version (provided that the files are intact and not  
damaged, which was also my first thought), but it is worth a try.

For one file, do
  library(affxparser)
  readCel(filename)

Kasper

>
>>
>> Best,
>>
>> Jim
>
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