[BioC] problem with R2.0.0

[Laurent Gautier]

James W. MacDonald wrote:
> Dianjing Guo wrote:
> 
>> Hi,
>>
>> I found the following error message while trying to read in 30 soybean 
>> cel files using R2.0.0:
>>
>> Error in initialize(value, ...) : End of file reached unexpectedly. 
>> Perhaps this file is truncated.
> 
> 
> I've never seen this error, but it looks like one of your cel files may 
> be corrupted.

This error testing was added to the (original) parsers to answer a 
specific problem (and robustify the code... 'was quite some time ago 
already..).
The problem was reported by Wolfgang Huber and Robert Gentleman (if I 
remember right), about CEL data they. They can probably tell more about 
why their data files were truncated.
(from experience, FTP transfers can sometimes play similar tricks)

> Another possibility is that you are running out of memory, 
> but you usually get a different error (I only mention this because IIRC, 
> the soybean chips are *huge*, so 30 of them might well use up all of 
> your RAM).

...this would mean that there is currently a memory leak in the parsers 
and/or a mishandling of the event (and a wrong error message)...

> Are any of your cel files very different in size? You might also try 
> reading in say 10 chips, then 15 chips etc until you locate the number 
> at which you hit the error. Then see if you can exclude that particular 
> chip and read in the remainder.

Using the flag "verbose" in 'read.affybatch' can be helpful (and spare 
you the recursive subdividing of the list of CEL files to find the problem).

> HTH,

'same,

L.

> Jim
> 
> 
>>
>> But i don't have problem read in small number of files (e.g 4 cel 
>> files). Is there any limit for the file size to be read in each time?
>> Any comments regarding this would be highly appreciated.
>>
>> Dianjing
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
>