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@jhsph.edu> > To: Simon Cawley <simon_cawley@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