Hi, This is interesting... I've tried to duplicate this with 2.1.3 from the devel library and the current release version and it works fine for me on windows and on linux. Please can you try updating to 2.1.3 and seeing if that fixes things? If not then let me know and we can try to explore things further. Best, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer Sent: 27 July 2005 00:33 To: Bioconductor Subject: [BioC] zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds I have a problem with simpleaffy and zebrafish: > all.raw AffyBatch object size of arrays=712x712 features (11889 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish > all.mas5 <- call.exprs(all.raw,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ...done. scaling to a TGT of 100 ... Scale factor for: EG Zebrafish control 20July05.CEL 1.07236539803815 Scale factor for: EG Zebrafish 310 20July05.CEL 1.14945565186904 Scale factor for: EG Zebrafish 820 20July05.CEL 1.04463357372716 > qc <- qc(all.raw,all.mas5) Getting probe level data... Computing p-values Doing PMA Calls Error in FUN(X[[4]], ...) : subscript out of bounds > sessionInfo() R version 2.1.1, 2005-07-10, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" [6] "utils" "datasets" "base" other attached packages: zebrafishprobe zebrafishcdf zebrafish qvalue "1.1" "1.5.1" "1.8.4" "1.1" gcrma matchprobes simpleaffy affy "1.1.4" "1.0.22" "2.1.1" "1.6.7" reposTools Biobase "1.5.19" "1.5.12" Thanks very much, 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 http://staff.washington.edu/~dbeyer _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi Crispin, Thanks for looking into this. I will have to wait until the windows version of 2.1.3 is available. Thanks much, 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 http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Wed, 27 Jul 2005, Crispin Miller wrote: > Hi, > This is interesting... I've tried to duplicate this with 2.1.3 from the > devel library and the current release version and it works fine for me > on windows and on linux. Please can you try updating to 2.1.3 and seeing > if that fixes things? > If not then let me know and we can try to explore things further. > Best, > > Crispin > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer > Sent: 27 July 2005 00:33 > To: Bioconductor > Subject: [BioC] zebrafish simpleaffy Error in FUN(X[[4]], ...) : > subscript out of bounds > > I have a problem with simpleaffy and zebrafish: > >> all.raw > AffyBatch object > size of arrays=712x712 features (11889 kb) cdf=Zebrafish (15617 affyids) > number of samples=3 number of genes=15617 annotation=zebrafish > >> all.mas5 <- call.exprs(all.raw,"mas5") > Background correcting > Retrieving data from AffyBatch...done. > Computing expression calls... > ...done. > scaling to a TGT of 100 ... > Scale factor for: EG Zebrafish control 20July05.CEL 1.07236539803815 > Scale factor for: EG Zebrafish 310 20July05.CEL 1.14945565186904 Scale > factor for: EG Zebrafish 820 20July05.CEL 1.04463357372716 >> qc <- qc(all.raw,all.mas5) > Getting probe level data... > Computing p-values > Doing PMA Calls > Error in FUN(X[[4]], ...) : subscript out of bounds > >> sessionInfo() > R version 2.1.1, 2005-07-10, i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" > [6] "utils" "datasets" "base" > > other attached packages: > zebrafishprobe zebrafishcdf zebrafish qvalue > "1.1" "1.5.1" "1.8.4" "1.1" > gcrma matchprobes simpleaffy affy > "1.1.4" "1.0.22" "2.1.1" "1.6.7" > reposTools Biobase > "1.5.19" "1.5.12" > > Thanks very much, > 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 > http://staff.washington.edu/~dbeyer > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use...{{dropped}}