[BioC] qc.stats error with mgu74av2

Dick Beyer dbeyer at u.washington.edu
Sun Feb 1 08:03:24 MET 2004

I have tried to use qc.stats from simpleaffy with mgu74av2 chips:

qc <- qc.stats(x.raw,x.mas5)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in cbind(det$call["AFFX-r2-Ec-bioB-3_at", ], det$call["AFFX-r2-Ec-bioC-3_at",  : subscript out of bounds

I believe AFFX-r2-Ec-bioB-3_at is on the hgu133 chip, but not the mgu74av2 chip.  The qc.stats code needs a switch for spikes that is chip dependent?

Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099

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