affxparser: writeTpmap error (in as.vector(y))
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@andreas-heinzel-2809
Last seen 10.5 years ago
hi, i'm trying to use readBpmap to read an affymetrix bpmap file and writeTpmap to save it as text-bpmap file. reading seems to work fine, but the writeTpmap function dies with the following error: Writing sequence AffxCtrl:v1;r2_Tag Fehler in as.vector(y) : Argument "y" fehlt (ohne Standardwert) i'm using: R 2.7 on Mac affxparser 1.12.2 tried: GeneChip Drosophila Tiling 1.0R Array Dm35b_MF_v02-3_BDGPv4h.bpmap (http://www.affymetrix.com/Auth/support/d ownloads/library_files/drosophila_tiling1r_libraryfile.zip) GeneChip Chromosome 21/22 1.0 Array Set Chrom21_22B_F_v04-2_NCBIv30.bpmap (http://www.affymetrix.com/Auth/support/downloads/library_files/chrom2 1_22_libraryfile.zip) Best regards Andreas
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@kasper-daniel-hansen-2979
Last seen 20 months ago
United States
This function is broken and (consulting svn) has been broken for a long time. A fix is reasonably easy, I will commit something later today. Thanks for the report. Kasper On May 20, 2008, at 9:52 AM, Andreas Heinzel wrote: > hi, > > i'm trying to use readBpmap to read an affymetrix bpmap file and > writeTpmap to save it as text-bpmap file. > > reading seems to work fine, but the writeTpmap function dies with > the following error: > Writing sequence AffxCtrl:v1;r2_Tag > Fehler in as.vector(y) : Argument "y" fehlt (ohne Standardwert) > > i'm using: > R 2.7 on Mac > affxparser 1.12.2 > > tried: > GeneChip Drosophila Tiling 1.0R Array > Dm35b_MF_v02-3_BDGPv4h.bpmap (http://www.affymetrix.com/Auth/support /downloads/library_files/drosophila_tiling1r_libraryfile.zip > ) > GeneChip Chromosome 21/22 1.0 Array Set > Chrom21_22B_F_v04-2_NCBIv30.bpmap > (http://www.affymetrix.com/Auth/support/downloads/library_files/chro m21_22_libraryfile.zip > ) > > Best regards > Andreas > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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I have committed a fix to the devel branch. The fixed version is 1.13.3. You should be able to get it soon. Just download it manually and install under R-2.7.0 if you want to avoid using R-devel. There is nothing that is dependent on anything in bioc-devel or r-devel. Kasper On May 20, 2008, at 7:22 PM, Kasper Daniel Hansen wrote: > This function is broken and (consulting svn) has been broken for a > long time. A fix is reasonably easy, I will commit something later > today. Thanks for the report. > > Kasper > > On May 20, 2008, at 9:52 AM, Andreas Heinzel wrote: > >> hi, >> >> i'm trying to use readBpmap to read an affymetrix bpmap file and >> writeTpmap to save it as text-bpmap file. >> >> reading seems to work fine, but the writeTpmap function dies with >> the following error: >> Writing sequence AffxCtrl:v1;r2_Tag >> Fehler in as.vector(y) : Argument "y" fehlt (ohne Standardwert) >> >> i'm using: >> R 2.7 on Mac >> affxparser 1.12.2 >> >> tried: >> GeneChip Drosophila Tiling 1.0R Array >> Dm35b_MF_v02-3_BDGPv4h.bpmap (http://www.affymetrix.com/Auth/suppor t/downloads/library_files/drosophila_tiling1r_libraryfile.zip >> ) >> GeneChip Chromosome 21/22 1.0 Array Set >> Chrom21_22B_F_v04-2_NCBIv30.bpmap >> (http://www.affymetrix.com/Auth/support/downloads/library_files/chr om21_22_libraryfile.zip >> ) >> >> Best regards >> Andreas >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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