Rsubread featureCounts question
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@james-w-macdonald-5106
Last seen 8 hours ago
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I am confused by this output from featureCounts(): > dat1 <- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE) > head(dat1$annotation) GeneID Chr Start End Strand Length 1 497097 chr1 3214482 3216968 - 2487 2 497097 chr1 3421702 3421901 - 200 3 497097 chr1 3670552 3671498 - 947 4 100503874 chr1 3647309 3650509 - 3201 5 100503874 chr1 3658847 3658904 - 58 6 100038431 chr1 3680155 3681788 + 1634 > head(dat1$counts) [,1] 497097 0 497097 0 497097 0 100503874 0 100503874 0 100038431 0 The help page indicates that this should result in output that has been aggregated over each gene, not each exon. > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affycoretools_1.34.0 KEGG.db_2.10.1 GO.db_2.10.1 [4] affy_1.40.0 ReportingTools_2.2.0 knitr_1.5 [7] edgeR_3.4.0 limma_3.18.0 org.Mm.eg.db_2.10.1 [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.24.0 [13] Biobase_2.22.0 BiocGenerics_0.8.0 Rsubread_1.12.0 [16] BiocInstaller_1.12.0 Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Wei Shi ★ 3.6k
@wei-shi-2183
Last seen 2 days ago
Australia/Melbourne/Olivia Newton-John …
Dear Jim, We found a bug in the C code which seemed to cause the problems you have encountered. We are now investigating this and will come up with a fix for them in the next few days. Thanks, Wei On Oct 23, 2013, at 8:21 AM, James W. MacDonald wrote: > I am confused by this output from featureCounts(): > > > dat1 <- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE) > > head(dat1$annotation) > GeneID Chr Start End Strand Length > 1 497097 chr1 3214482 3216968 - 2487 > 2 497097 chr1 3421702 3421901 - 200 > 3 497097 chr1 3670552 3671498 - 947 > 4 100503874 chr1 3647309 3650509 - 3201 > 5 100503874 chr1 3658847 3658904 - 58 > 6 100038431 chr1 3680155 3681788 + 1634 > > head(dat1$counts) > [,1] > 497097 0 > 497097 0 > 497097 0 > 100503874 0 > 100503874 0 > 100038431 0 > > The help page indicates that this should result in output that has been aggregated over each gene, not each exon. > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] affycoretools_1.34.0 KEGG.db_2.10.1 GO.db_2.10.1 > [4] affy_1.40.0 ReportingTools_2.2.0 knitr_1.5 > [7] edgeR_3.4.0 limma_3.18.0 org.Mm.eg.db_2.10.1 > [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.24.0 > [13] Biobase_2.22.0 BiocGenerics_0.8.0 Rsubread_1.12.0 > [16] BiocInstaller_1.12.0 > > Best, > > Jim > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
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Wei Shi ★ 3.6k
@wei-shi-2183
Last seen 2 days ago
Australia/Melbourne/Olivia Newton-John …
Dear Jim, We have fixed the problems you have encountered and committed the changes to the release version of Rsubread (1.12.1). It should be available in a couple of days. Best regards, Wei On Oct 23, 2013, at 8:21 AM, James W. MacDonald wrote: > I am confused by this output from featureCounts(): > > > dat1 <- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE) > > head(dat1$annotation) > GeneID Chr Start End Strand Length > 1 497097 chr1 3214482 3216968 - 2487 > 2 497097 chr1 3421702 3421901 - 200 > 3 497097 chr1 3670552 3671498 - 947 > 4 100503874 chr1 3647309 3650509 - 3201 > 5 100503874 chr1 3658847 3658904 - 58 > 6 100038431 chr1 3680155 3681788 + 1634 > > head(dat1$counts) > [,1] > 497097 0 > 497097 0 > 497097 0 > 100503874 0 > 100503874 0 > 100038431 0 > > The help page indicates that this should result in output that has been aggregated over each gene, not each exon. > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] affycoretools_1.34.0 KEGG.db_2.10.1 GO.db_2.10.1 > [4] affy_1.40.0 ReportingTools_2.2.0 knitr_1.5 > [7] edgeR_3.4.0 limma_3.18.0 org.Mm.eg.db_2.10.1 > [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.24.0 > [13] Biobase_2.22.0 BiocGenerics_0.8.0 Rsubread_1.12.0 > [16] BiocInstaller_1.12.0 > > Best, > > Jim > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
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Thanks Wei! On Friday, October 25, 2013 8:18:44 AM, Wei Shi wrote: > Dear Jim, > > We have fixed the problems you have encountered and committed the changes to the release version of Rsubread (1.12.1). It should be available in a couple of days. > > Best regards, > Wei > > On Oct 23, 2013, at 8:21 AM, James W. MacDonald wrote: > >> I am confused by this output from featureCounts(): >> >>> dat1 <- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE) >>> head(dat1$annotation) >> GeneID Chr Start End Strand Length >> 1 497097 chr1 3214482 3216968 - 2487 >> 2 497097 chr1 3421702 3421901 - 200 >> 3 497097 chr1 3670552 3671498 - 947 >> 4 100503874 chr1 3647309 3650509 - 3201 >> 5 100503874 chr1 3658847 3658904 - 58 >> 6 100038431 chr1 3680155 3681788 + 1634 >>> head(dat1$counts) >> [,1] >> 497097 0 >> 497097 0 >> 497097 0 >> 100503874 0 >> 100503874 0 >> 100038431 0 >> >> The help page indicates that this should result in output that has been aggregated over each gene, not each exon. >> >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] affycoretools_1.34.0 KEGG.db_2.10.1 GO.db_2.10.1 >> [4] affy_1.40.0 ReportingTools_2.2.0 knitr_1.5 >> [7] edgeR_3.4.0 limma_3.18.0 org.Mm.eg.db_2.10.1 >> [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.24.0 >> [13] Biobase_2.22.0 BiocGenerics_0.8.0 Rsubread_1.12.0 >> [16] BiocInstaller_1.12.0 >> >> Best, >> >> Jim >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> _______________________________________________ >> 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 > > ______________________________________________________________________ > The information in this email is confidential and intended solely for the addressee. > You must not disclose, forward, print or use it without the permission of the sender. > ______________________________________________________________________ -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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