[BioC] read.affybatch fails with DrosGenome1 chips

[James MacDonald]

Hi all,

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:

[HEADER]
Cols=640
Rows=640
TotalX=640
TotalY=640
OffsetX=0
OffsetY=0
GridCornerUL=234 232
GridCornerUR=4497 196
GridCornerLR=4535 4461
GridCornerLL=272 4496
Axis-invertX=0
AxisInvertY=0
swapXY=0
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         
                 6
Algorithm=Percentile
AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004

Regards,

Jim




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623