Question: dmrFinder error
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5.6 years ago by
Guest User12k
Guest User12k wrote:
dear all, I was trying to apply dmrFinder function in bsseq package, but it always gives the following error: ################################################## dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6)) segmenting splitting creating dmr data.frame Error in ifelse(regions$meanDiff > 0, "hyper", "hypo") : error in evaluating the argument 'test' in selecting a method for function 'ifelse': Error in regions$meanDiff : $ operator is invalid for atomic vectors ################################################## The code is from http://www.bioconductor.org/packages/2.13/bioc/vignet tes/bsseq/inst/doc/bsseq_analysis.R Thank you for any solution! best, Jun -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-suse-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] bsseqData_0.1.3 bsseq_0.8.0 matrixStats_0.8.5 GenomicRanges_1.12.4 [5] IRanges_1.18.2 BiocGenerics_0.6.0 BiocInstaller_1.10.4 seqinr_3.0-7 loaded via a namespace (and not attached): [1] Biobase_2.20.1 colorspace_1.2-4 dichromat_2.0-0 grid_3.0.1 labeling_0.2 [6] lattice_0.20-15 locfit_1.5-9.1 munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 [11] R.methodsS3_1.5.2 scales_0.2.3 stats4_3.0.1 stringr_0.6.2 tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 5.6 years ago by Kasper Daniel Hansen6.4k • written 5.6 years ago by Guest User12k
Answer: dmrFinder error
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gravatar for Kasper Daniel Hansen
5.6 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
That code is executed when the package is being build on the build server - ie. it runs on the build server. Having said that, I vaguely recalling seeing this error before. I see you are running an old version of bsseq though, so I would suggest updating to the newest Bioconductor release, and also checking using biocValid() that all your packages are the right version. If you still get the error after doing this, you should report back Best, Kasper On Tue, Oct 29, 2013 at 7:52 PM, genefan [guest] <guest@bioconductor.org>wrote: > > dear all, > > I was trying to apply dmrFinder function in bsseq package, but it always > gives the following error: > > ################################################## > dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6)) > segmenting > splitting > creating dmr data.frame > Error in ifelse(regions$meanDiff > 0, "hyper", "hypo") : > error in evaluating the argument 'test' in selecting a method for > function 'ifelse': Error in regions$meanDiff : $ operator is invalid for > atomic vectors > ################################################## > The code is from > http://www.bioconductor.org/packages/2.13/bioc/vignettes/bsseq/inst/ doc/bsseq_analysis.R > > Thank you for any solution! > best, > Jun > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-suse-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] bsseqData_0.1.3 bsseq_0.8.0 matrixStats_0.8.5 > GenomicRanges_1.12.4 > [5] IRanges_1.18.2 BiocGenerics_0.6.0 BiocInstaller_1.10.4 > seqinr_3.0-7 > > loaded via a namespace (and not attached): > [1] Biobase_2.20.1 colorspace_1.2-4 dichromat_2.0-0 grid_3.0.1 > labeling_0.2 > [6] lattice_0.20-15 locfit_1.5-9.1 munsell_0.4.2 plyr_1.8 > RColorBrewer_1.0-5 > [11] R.methodsS3_1.5.2 scales_0.2.3 stats4_3.0.1 > stringr_0.6.2 tools_3.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.6 years ago by Kasper Daniel Hansen6.4k
Thank you! After updating the package, the problem is solved. On Wed, Oct 30, 2013 at 4:35 AM, Kasper Daniel Hansen <khansen@jhsph.edu>wrote: > That code is executed when the package is being build on the build server > - ie. it runs on the build server. Having said that, I vaguely recalling > seeing this error before. > > I see you are running an old version of bsseq though, so I would suggest > updating to the newest Bioconductor release, and also checking using > biocValid() > that all your packages are the right version. If you still get the error > after doing this, you should report back > > Best, > Kasper > > > On Tue, Oct 29, 2013 at 7:52 PM, genefan [guest] <guest@bioconductor.org>wrote: > >> >> dear all, >> >> I was trying to apply dmrFinder function in bsseq package, but it always >> gives the following error: >> >> ################################################## >> dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6)) >> segmenting >> splitting >> creating dmr data.frame >> Error in ifelse(regions$meanDiff > 0, "hyper", "hypo") : >> error in evaluating the argument 'test' in selecting a method for >> function 'ifelse': Error in regions$meanDiff : $ operator is invalid for >> atomic vectors >> ################################################## >> The code is from >> http://www.bioconductor.org/packages/2.13/bioc/vignettes/bsseq/inst /doc/bsseq_analysis.R >> >> Thank you for any solution! >> best, >> Jun >> >> -- output of sessionInfo(): >> >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-suse-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 >> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 >> LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] bsseqData_0.1.3 bsseq_0.8.0 matrixStats_0.8.5 >> GenomicRanges_1.12.4 >> [5] IRanges_1.18.2 BiocGenerics_0.6.0 BiocInstaller_1.10.4 >> seqinr_3.0-7 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.20.1 colorspace_1.2-4 dichromat_2.0-0 grid_3.0.1 >> labeling_0.2 >> [6] lattice_0.20-15 locfit_1.5-9.1 munsell_0.4.2 plyr_1.8 >> RColorBrewer_1.0-5 >> [11] R.methodsS3_1.5.2 scales_0.2.3 stats4_3.0.1 >> stringr_0.6.2 tools_3.0.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by Junfang Chen10
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