[BioC] read.affybatch fails with DrosGenome1 chips
jmacdon at med.umich.edu
Fri Oct 3 12:26:56 MEST 2003
When I use newer versions of read.affybatch that use calls to the C
function ReadHeader (read.affybatch2 in older versions of affy,
read.affybatch in the CVS version), to read in DrosGenome1 chips, R
completely bombs out and I get the 'Tell Microsoft about this
problem...' message box. AFAIK, this doesn't happen with any other cel
file type (U133A/B, MOEA/B, RAEA/B, celegans, U95v2A, RG-U34A, etc.).
Using debug() I have tracked it down to the call to ReadHeader.
I don't know C very well at all, so I am not sure where the problem
lies, but I wonder if it has something to do with the fact that the cdf
name for drosgenome is DrosGenome1.1sq and get_header_info is trying to
strip off the .1sq portion?
Here is the relevant header portion from the cel file:
DatHeader=[0..46144] Cadigan_001:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17
2.0 08/29/03 15:44:31 DrosGenome1.1sq
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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