Question: zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
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gravatar for Dick Beyer
14.2 years ago by
Dick Beyer1.4k
Dick Beyer1.4k wrote:
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
ADD COMMENTlink modified 14.2 years ago by Ting-Yuan Liu FHCRC780 • written 14.2 years ago by Dick Beyer1.4k
Answer: zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
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gravatar for Ting-Yuan Liu FHCRC
14.2 years ago by
Ting-Yuan Liu FHCRC780 wrote:
Hi Dick, Could you provide more information about your code? I try to reproduce the error, but I cannot. I don't know how you created the AffyBatch object "all.raw". If you can provide the complete code, it will be helpful. Ting-Yuan On Tue, 26 Jul 2005, Dick Beyer wrote: > 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 >
ADD COMMENTlink written 14.2 years ago by Ting-Yuan Liu FHCRC780
Hi Ting-Yuan, I started a new session of R and was unable to reproduce my own error. Even though the packages are the same. Most strange. I am very sorry you and Crispin Miller had to bother with this, and thanks for solving my problem, operator error. 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 ********************************************************************** ********* On Thu, 28 Jul 2005, Ting-Yuan Liu (FHCRC) wrote: > > Hi Dick, > > Could you provide more information about your code? I try to reproduce > the error, but I cannot. I don't know how you created the AffyBatch > object "all.raw". If you can provide the complete code, it will be > helpful. > > Ting-Yuan > > On Tue, 26 Jul 2005, Dick Beyer wrote: > >> 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 >> >
ADD REPLYlink written 14.2 years ago by Dick Beyer1.4k
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