[BioC] problem with R2.0.0

[James W. MacDonald]

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. 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).

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.

HTH,

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
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109