Combine function in matchprobes
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Tan, MinHan ▴ 180
@tan-minhan-431
Last seen 8.1 years ago
Hi, I tried combining 2 Affybatches (HGU133A and HGU133Plus 2.0) using combine in matchprobes, but ran into the following problems. I used both R 1.9.0 and R 1.8.1 with the latest downloads from Bioconductor. > merged.data <- combine(list(DataHGU133A,DataHGU133P), c("hgu133acdf", "hgu133plus2cdf"), "mycdf", verbose=TRUE) package:hgu133acdf hgu133acdf package:hgu133plus2cdf hgu133plus2cdf 0 probes in common between hgu133acdf and hgu133acdf Error in sequs[[i]] : subscript out of bounds Looking at the combine function, I seem to be running into problems at this point? > tmp <- get(upp[1], uppname[1]) > str(tmp) length 0 <environment> > upp[1] [1] "hgu133acdf" > uppname[1] [1] "package:hgu133acdf" Your advice is very much appreciated! Min-Han Tan This email message, including any attachments, is for the so...{{dropped}}
cdf matchprobes cdf matchprobes • 634 views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 7.4 years ago
United States
Well, the man page for combine says: Usage: combine(batch, probepkg, newcdf, verbose=TRUE) Arguments: batch: A 'list' of AffyBatches. probepkg: A character vector of the same length as 'batch', containing the names of the probe sequences libraries (for example, 'hgu133aprobe') that go with the AffyBatches. newcdf: Character. The name of the name CDF environment that is to be created. verbose: Logical. If TRUE, messages are printed to the console. And I do not see where you have indicated the probe packages? You do need them (and they are available on the Bioconductor site). Robert On Fri, Jan 16, 2004 at 03:03:27PM -0500, Tan, MinHan wrote: > Hi, > > I tried combining 2 Affybatches (HGU133A and HGU133Plus 2.0) using > combine in matchprobes, but ran into the following problems. > > I used both R 1.9.0 and R 1.8.1 with the latest downloads from > Bioconductor. > > > merged.data <- combine(list(DataHGU133A,DataHGU133P), c("hgu133acdf", > "hgu133plus2cdf"), "mycdf", verbose=TRUE) > package:hgu133acdf hgu133acdf > package:hgu133plus2cdf hgu133plus2cdf > 0 probes in common between hgu133acdf and hgu133acdf > Error in sequs[[i]] : subscript out of bounds > > Looking at the combine function, I seem to be running into problems at > this point? > > > tmp <- get(upp[1], uppname[1]) > > str(tmp) > length 0 <environment> > > upp[1] > [1] "hgu133acdf" > > uppname[1] > [1] "package:hgu133acdf" > > > Your advice is very much appreciated! > > > Min-Han Tan > > This email message, including any attachments, is for the so...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+
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Hi Min-Han Tan, You specified CDF packages instead of probe packages. The combine function will produce a more intelligible error message rather than the one you reported in version 1.0.3 which will be on the web shortly. Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- On Fri, 16 Jan 2004, Robert Gentleman wrote: > Well, the man page for combine says: > Usage: > > combine(batch, probepkg, newcdf, verbose=TRUE) > > Arguments: > > batch: A 'list' of AffyBatches. > > probepkg: A character vector of the same length as 'batch', containing > the names of the probe sequences libraries (for example, > 'hgu133aprobe') that go with the AffyBatches. > > newcdf: Character. The name of the name CDF environment that is to > be > created. > > verbose: Logical. If TRUE, messages are printed to the console. > > > And I do not see where you have indicated the probe packages? > You do need them (and they are available on the Bioconductor site). > > Robert > > > On Fri, Jan 16, 2004 at 03:03:27PM -0500, Tan, MinHan wrote: > > Hi, > > > > I tried combining 2 Affybatches (HGU133A and HGU133Plus 2.0) using > > combine in matchprobes, but ran into the following problems. > > > > I used both R 1.9.0 and R 1.8.1 with the latest downloads from > > Bioconductor. > > > > > merged.data <- combine(list(DataHGU133A,DataHGU133P), c("hgu133acdf", > > "hgu133plus2cdf"), "mycdf", verbose=TRUE) > > package:hgu133acdf hgu133acdf > > package:hgu133plus2cdf hgu133plus2cdf > > 0 probes in common between hgu133acdf and hgu133acdf > > Error in sequs[[i]] : subscript out of bounds > > > > Looking at the combine function, I seem to be running into problems at > > this point? > > > > > tmp <- get(upp[1], uppname[1]) > > > str(tmp) > > length 0 <environment> > > > upp[1] > > [1] "hgu133acdf" > > > uppname[1] > > [1] "package:hgu133acdf" > > > > > > Your advice is very much appreciated! > > > > > > Min-Han Tan > > > > This email message, including any attachments, is for the so...{{dropped}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------------- --------+ > | Robert Gentleman phone : (617) 632-5250 | > | Associate Professor fax: (617) 632-2444 | > | Department of Biostatistics office: M1B20 | > | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | > +------------------------------------------------------------------- --------+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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