Oligo package, possible bug in paCalls

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James Perkins ▴ 120

@james-perkins-4948

Last seen 9.6 years ago

Dear Benilton, I had a problem running paCalls() from the oligo package, specifically I got: Error in dimnames(res) <- list(fid, sampleNames(x)) : length of 'dimnames' [1] not equal to array extent > if (require(oligoData) & require(pd.huex.1.0.st.v2)){ + data(affyExonFS) + ## Get only 2 samples for example + dabgP = paCalls(affyExonFS[, 1:2]) + dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG") + head(dabgP) ## for probe + head(dabgPS) ## for probeset + } Loading required package: oligoData Loading required package: pd.huex.1.0.st.v2 Loading required package: RSQLite Loading required package: DBI Computing DABG calls... Error in dimnames(res) <- list(fid, sampleNames(x)) : length of 'dimnames' [1] not equal to array extent > traceback() 4: paFun(object) 3: .local(object, method, ..., verbose) 2: paCalls(affyExonFS[, 1:2]) at #4 1: paCalls(affyExonFS[, 1:2]) at #4 > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.huex.1.0.st.v2_3.6.0 RSQLite_0.11.1 DBI_0.2-5 [4] oligoData_1.6.0 oligo_1.20.3 oligoClasses_1.18.0 loaded via a namespace (and not attached): [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 [4] BiocGenerics_0.2.0 BiocInstaller_1.4.7 Biostrings_2.24.1 [7] bit_1.1-8 codetools_0.2-8 ff_2.2-7 [10] foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 [16] tools_2.15.0 zlibbioc_1.2.0 > I can confirm it worked as expected with R-2.13.0, so I assume this is a bug? Many thanks, Jim -- James Perkins Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Street London, WC1E 6BT UK email: j.perkins at ucl.ac.uk

oligo oligo • 1.0k views

ADD COMMENT • link updated 11.8 years ago by Benilton Carvalho ★ 4.3k • written 11.8 years ago by James Perkins ▴ 120

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Benilton Carvalho ★ 4.3k

@benilton-carvalho-1375

Last seen 4.1 years ago

Brazil/Campinas/UNICAMP

thanks for the report, will get back to you asap. b On 4 July 2012 11:58, James Perkins <j.perkins at="" ucl.ac.uk=""> wrote: > Dear Benilton, > > I had a problem running paCalls() from the oligo package, specifically I got: > > Error in dimnames(res) <- list(fid, sampleNames(x)) : > length of 'dimnames' [1] not equal to array extent > >> if (require(oligoData) & require(pd.huex.1.0.st.v2)){ > + data(affyExonFS) > + ## Get only 2 samples for example > + dabgP = paCalls(affyExonFS[, 1:2]) > + dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG") > + head(dabgP) ## for probe > + head(dabgPS) ## for probeset > + } > Loading required package: oligoData > Loading required package: pd.huex.1.0.st.v2 > Loading required package: RSQLite > Loading required package: DBI > Computing DABG calls... Error in dimnames(res) <- list(fid, sampleNames(x)) : > length of 'dimnames' [1] not equal to array extent >> traceback() > 4: paFun(object) > 3: .local(object, method, ..., verbose) > 2: paCalls(affyExonFS[, 1:2]) at #4 > 1: paCalls(affyExonFS[, 1:2]) at #4 >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.huex.1.0.st.v2_3.6.0 RSQLite_0.11.1 DBI_0.2-5 > [4] oligoData_1.6.0 oligo_1.20.3 oligoClasses_1.18.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 > [4] BiocGenerics_0.2.0 BiocInstaller_1.4.7 Biostrings_2.24.1 > [7] bit_1.1-8 codetools_0.2-8 ff_2.2-7 > [10] foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 > [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 > [16] tools_2.15.0 zlibbioc_1.2.0 >> > > I can confirm it worked as expected with R-2.13.0, so I assume this is a bug? > > Many thanks, > > Jim > -- > James Perkins > Institute of Structural and Molecular Biology > Division of Biosciences > University College London > Gower Street > London, WC1E 6BT > UK > > email: j.perkins at ucl.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 11.8 years ago Benilton Carvalho ★ 4.3k

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this has been addressed on oligo 1.20.4, which should appear online soon. b On 4 July 2012 12:01, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > thanks for the report, will get back to you asap. b > > On 4 July 2012 11:58, James Perkins <j.perkins at="" ucl.ac.uk=""> wrote: >> Dear Benilton, >> >> I had a problem running paCalls() from the oligo package, specifically I got: >> >> Error in dimnames(res) <- list(fid, sampleNames(x)) : >> length of 'dimnames' [1] not equal to array extent >> >>> if (require(oligoData) & require(pd.huex.1.0.st.v2)){ >> + data(affyExonFS) >> + ## Get only 2 samples for example >> + dabgP = paCalls(affyExonFS[, 1:2]) >> + dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG") >> + head(dabgP) ## for probe >> + head(dabgPS) ## for probeset >> + } >> Loading required package: oligoData >> Loading required package: pd.huex.1.0.st.v2 >> Loading required package: RSQLite >> Loading required package: DBI >> Computing DABG calls... Error in dimnames(res) <- list(fid, sampleNames(x)) : >> length of 'dimnames' [1] not equal to array extent >>> traceback() >> 4: paFun(object) >> 3: .local(object, method, ..., verbose) >> 2: paCalls(affyExonFS[, 1:2]) at #4 >> 1: paCalls(affyExonFS[, 1:2]) at #4 >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.huex.1.0.st.v2_3.6.0 RSQLite_0.11.1 DBI_0.2-5 >> [4] oligoData_1.6.0 oligo_1.20.3 oligoClasses_1.18.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 >> [4] BiocGenerics_0.2.0 BiocInstaller_1.4.7 Biostrings_2.24.1 >> [7] bit_1.1-8 codetools_0.2-8 ff_2.2-7 >> [10] foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 >> [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 >> [16] tools_2.15.0 zlibbioc_1.2.0 >>> >> >> I can confirm it worked as expected with R-2.13.0, so I assume this is a bug? >> >> Many thanks, >> >> Jim >> -- >> James Perkins >> Institute of Structural and Molecular Biology >> Division of Biosciences >> University College London >> Gower Street >> London, WC1E 6BT >> UK >> >> email: j.perkins at ucl.ac.uk >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 11.8 years ago Benilton Carvalho ★ 4.3k

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Thanks for the speedy fix! I downloaded from svn and so far it seems to be working ok. Cheers, Jim On 4 July 2012 17:49, Benilton Carvalho <beniltoncarvalho@gmail.com> wrote: > this has been addressed on oligo 1.20.4, which should appear online soon. b > > On 4 July 2012 12:01, Benilton Carvalho <beniltoncarvalho@gmail.com> > wrote: > > thanks for the report, will get back to you asap. b > > > > On 4 July 2012 11:58, James Perkins <j.perkins@ucl.ac.uk> wrote: > >> Dear Benilton, > >> > >> I had a problem running paCalls() from the oligo package, specifically > I got: > >> > >> Error in dimnames(res) <- list(fid, sampleNames(x)) : > >> length of 'dimnames' [1] not equal to array extent > >> > >>> if (require(oligoData) & require(pd.huex.1.0.st.v2)){ > >> + data(affyExonFS) > >> + ## Get only 2 samples for example > >> + dabgP = paCalls(affyExonFS[, 1:2]) > >> + dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG") > >> + head(dabgP) ## for probe > >> + head(dabgPS) ## for probeset > >> + } > >> Loading required package: oligoData > >> Loading required package: pd.huex.1.0.st.v2 > >> Loading required package: RSQLite > >> Loading required package: DBI > >> Computing DABG calls... Error in dimnames(res) <- list(fid, > sampleNames(x)) : > >> length of 'dimnames' [1] not equal to array extent > >>> traceback() > >> 4: paFun(object) > >> 3: .local(object, method, ..., verbose) > >> 2: paCalls(affyExonFS[, 1:2]) at #4 > >> 1: paCalls(affyExonFS[, 1:2]) at #4 > >>> sessionInfo() > >> R version 2.15.0 (2012-03-30) > >> Platform: x86_64-unknown-linux-gnu (64-bit) > >> > >> locale: > >> [1] LC_CTYPE=en_US LC_NUMERIC=C > >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > >> [7] LC_PAPER=C LC_NAME=C > >> [9] LC_ADDRESS=C LC_TELEPHONE=C > >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] pd.huex.1.0.st.v2_3.6.0 RSQLite_0.11.1 DBI_0.2-5 > >> [4] oligoData_1.6.0 oligo_1.20.3 oligoClasses_1.18.0 > >> > >> loaded via a namespace (and not attached): > >> [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 > >> [4] BiocGenerics_0.2.0 BiocInstaller_1.4.7 Biostrings_2.24.1 > >> [7] bit_1.1-8 codetools_0.2-8 ff_2.2-7 > >> [10] foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 > >> [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 > >> [16] tools_2.15.0 zlibbioc_1.2.0 > >>> > >> > >> I can confirm it worked as expected with R-2.13.0, so I assume this is > a bug? > >> > >> Many thanks, > >> > >> Jim > >> -- > >> James Perkins > >> Institute of Structural and Molecular Biology > >> Division of Biosciences > >> University College London > >> Gower Street > >> London, WC1E 6BT > >> UK > >> > >> email: j.perkins@ucl.ac.uk > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James Perkins Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Street London, WC1E 6BT UK email: j.perkins@ucl.ac.uk [[alternative HTML version deleted]]

ADD REPLY • link 11.8 years ago James Perkins ▴ 120

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