Question: read.affybatch fails with DrosGenome1 chips
gravatar for James W. MacDonald
16.1 years ago by
United States
James W. MacDonald51k wrote:
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;Outli erLow: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
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