[BioC] qc.stats error with mgu74av2

[Crispin Miller]

Hi Dick,
Yup - that was an error in the old version... The newest version on the
site (1.03) has just the switch you suggest (It only handles murine and
human arrays at the moment...):

  if(n %in% c("hgu133acdf", "hgu133atagcdf", "hgu133bcdf",
"hgu133plus2cdf", "hgu95acdf", 
              "hgu95av2cdf", "hgu95bcdf", "hgu95ccdf", "hgu95dcdf",
"hgu95ecdf")) {
    rats <- 2^cbind((x["AFFX-HUMGAPDH/M33197_3_at",] -
x["AFFX-HUMGAPDH/M33197_5_at",]),
                    (x["AFFX-HUMGAPDH/M33197_3_at",] -
x["AFFX-HUMGAPDH/M33197_M_at",]),
                    (x["AFFX-HSAC07/X00351_3_at",]  -
x["AFFX-HSAC07/X00351_5_at",]),
                    (x["AFFX-HSAC07/X00351_3_at",]  -
x["AFFX-HSAC07/X00351_M_at",]));

  }
  else {
    if (n %in% c("mgu74acdf", "mgu74av2cdf", "mgu74bcdf", "mgu74bv2cdf",
"mgu74ccdf", "mgu74cv2cdf", "moe430acdf", "moe430bcdf", "mu19kcdf")) {
      rats <- 2^cbind((x["AFFX-GapdhMur/M32599_3_at",] -
x["AFFX-GapdhMur/M32599_5_at",]),
                      (x["AFFX-GapdhMur/M32599_3_at",] -
x["AFFX-GapdhMur/M32599_M_at",]),
                      (x["AFFX-b-ActinMur/M12481_3_at",]  -
x["AFFX-b-ActinMur/M12481_5_at",]),
                     (x["AFFX-b-ActinMur/M12481_3_at",]  -
x["AFFX-b-ActinMur/M12481_M_at",]));
    }
  
    else { stop(paste("Sorry - I'm afraid I don't know about the spike
probes on '",n,"' arrays.")) }


I've also fixed loads of other little bugs and stuff, so it's most
definitely a good idea to pull down the latest version...:-)

Cheers,
Crispin


-----Original Message-----
From: Dick Beyer [mailto:dbeyer at u.washington.edu] 
Sent: 01 February 2004 07:03
To: Bioconductor
Subject: [BioC] qc.stats error with mgu74av2


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?

Thanks,
Dick
************************************************************************
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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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