[BioC] Re: affy package problem

[Simon Cawley]

Sure, and thanks for the tip on read.affybatch2

affy package developers, please see below for a bug report.

Thanks,

-Simon


On Tue, 1 Jul 2003, Rafael A. Irizarry wrote:

> Date: Tue, 01 Jul 2003 14:50:50 -0400 (EDT)
> From: Rafael A. Irizarry <ririzarr at jhsph.edu>
> To: Simon Cawley <simon_cawley at affymetrix.com>
> Subject: Re: affy package problem
> 
> thanks for the bug report. do you mind sending this to the bioconductor 
> mailing list? 
> 
> also, the latest version (1.3.3) has a function called read.affybatch2 
> that is much faster and memory efficient than the current read.affybatch
> 
> -rafael
> 
> On Tue, 1 Jul 2003, Simon 
> Cawley wrote:
> 
> > 
> > Hey Rafa, 
> > 
> > As affy package maintainer perhaps you can fix a problem I'm running into.  I have some U133 files I can't open with read.affybatch - I get the following error:
> > 
> >   could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) 
> > 
> > I've tracked it down to the following line in read_cdffile.c
> > 
> >   #define SIZE_LINE 160 /* line buffer length...  too short ? */
> > 
> > This particular CEL file has a really long file name, which seems to make the DatHeader entry very long:
> > 
> >   DatHeader=[0..59005]  12_13_02_U133A_Mer_Latin_Square_Expt1_R1:CLS=5400 RWS=5400 XIN=2  YIN=2  VE=30        2.0 12/13/02 15:06:26 50101250  M18   s  s HG-U133A_.1sq s  s  s  s  s  s  s  s  s 6
> > 
> > but a call to getInfoInAffyFile() returns the following:
> > 
> > [1] "[0..59005]  12_13_02_U133A_Mer_Latin_Square_Expt1_R1:CLS=5400 RWS=5400 XIN=2  YIN=2  VE=30        2.0 12/13/02 15:06:26 50101250  M18   s  s HG-U133"
> > 
> > Note that "HG-U133A_.1sq" got truncated to "HG-U133" which I think is the reason for the problem.  I'm not sure how big the value should be to avoid this in general, I bumped it up to 1024 and then it worked for me.
> > 
> > -S