qc.stats error with mgu74av2
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Dick Beyer ★ 1.4k
@dick-beyer-26
Last seen 7.3 years ago
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 ********************************************************************** ********* 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
mgu74av2 probe simpleaffy mgu74av2 probe simpleaffy • 684 views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
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@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 ********************************************************************** ** ******* 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
Hi Dick - sorry - entirely my mistake: I'll fix it and get back to you ;-) Cheers, Crispin -----Original Message----- From: Dick Beyer [mailto:dbeyer@u.washington.edu] Sent: 02 February 2004 17:37 To: Crispin Miller Subject: RE: [BioC] qc.stats error with mgu74av2 Hi Crispin, The bug I found was in 1.03. The problem is in the spikes assignment line: spikes <- cbind(det$call["AFFX-r2-Ec-bioB-3_at", ], det$call["AFFX-r2-Ec-bioC-3_at", ], det$call["AFFX-r2-Ec-bioD-3_at", ], det$call["AFFX-r2-P1-cre-3_at", ]) I don't believe "AFFX-r2-Ec-bioB-3_at" is on the mgu74av2 chip. Thanks, Dick ********************************************************************** ** ******* 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html ********************************************************************** ** ******* On Mon, 2 Feb 2004, Crispin Miller wrote: > 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@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 > ********************************************************************** > ** > ******* > 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 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use of the > person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the Christie Hospital NHS Trust. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible. > > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
OK - I think I've fixed it. I get identical results on u74 data between the Affy software and qc.stats... A new version will appear in devl in the goodness of time :-) Cherio, Crispin -----Original Message----- From: Crispin Miller Sent: 03 February 2004 10:27 To: Dick Beyer Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] qc.stats error with mgu74av2 Hi Dick - sorry - entirely my mistake: I'll fix it and get back to you ;-) Cheers, Crispin -----Original Message----- From: Dick Beyer [mailto:dbeyer@u.washington.edu] Sent: 02 February 2004 17:37 To: Crispin Miller Subject: RE: [BioC] qc.stats error with mgu74av2 Hi Crispin, The bug I found was in 1.03. The problem is in the spikes assignment line: spikes <- cbind(det$call["AFFX-r2-Ec-bioB-3_at", ], det$call["AFFX-r2-Ec-bioC-3_at", ], det$call["AFFX-r2-Ec-bioD-3_at", ], det$call["AFFX-r2-P1-cre-3_at", ]) I don't believe "AFFX-r2-Ec-bioB-3_at" is on the mgu74av2 chip. Thanks, Dick ********************************************************************** ** ******* 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html ********************************************************************** ** ******* On Mon, 2 Feb 2004, Crispin Miller wrote: > 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@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 > ********************************************************************** > ** > ******* > 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 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use of the > person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the Christie Hospital NHS Trust. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible. > > -------------------------------------------------------- This email is confidential and intended solely for the use\ ...{{dropped}}
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