Question about ReportingTools used with DESeq2
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@amandinefournierchu-lyonfr-5921
Last seen 7.1 years ago
Hi, I am currently using the last version of the DESeq2 package to analyse some RNA-Seq data. I would like to use the ReportingTools package to export the results, but I am facing a warning. My code is : > library("DESeq2") > sampleFiles = c("htseqcount_Sample_1.txt","htseqcount_Sample_2.txt", "htseqcount_Sample_3.txt","htseqcount_Sample_4.txt") > sampleCondition = c("case","control","case","control") > sampleNames = c("Sample_1","Sample_2","Sample_3","Sample_4") > sampleTable <- data.frame(sampleName = sampleNames, fileName = sampleFiles, condition = sampleCondition) > dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = "./", design = ~ condition) > colData(dds)$condition = factor(colData(dds)$condition, levels = c("control","case")) > dds <- DESeq(dds) > res <- results(dds) > library(ReportingTools) > library("BSgenome.Hsapiens.UCSC.hg19") > des2Report <- HTMLReport(shortName='RNAseq_analysis_with_DESeq2', title='RNA-seq analysis of differential expression', reportDirectory="./reports") > publish(dds, des2Report, pvalueCutoff=0.05, annotation.db="BSgenome.Hsapiens.UCSC.hg19", factor = colData(dds)$conditions, reportDir="./reports") Message d'avis : In cols(db) : 'cols' has been deprecated and replaced by 'columns' for versions of Bioc that are higher than 2.13. Please use 'columns' anywhere that you previously used 'cols' Does anybody known what is wrong and how to fix it ? Here is my sessionInfo() : R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 [5] LC_MONETARY=fr_FR.utf8 LC_MESSAGES=fr_FR.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0 [3] Biostrings_2.30.1 ReportingTools_2.2.0 [5] AnnotationDbi_1.24.0 Biobase_2.22.0 [7] RSQLite_0.11.4 DBI_0.2-7 [9] knitr_1.5 DESeq2_1.2.5 [11] RcppArmadillo_0.3.920.3 Rcpp_0.10.6 [13] GenomicRanges_1.14.3 XVector_0.2.0 [15] IRanges_1.20.5 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationForge_1.4.4 biomaRt_2.18.0 [4] biovizBase_1.10.3 bitops_1.0-6 Category_2.28.0 [7] cluster_1.14.4 colorspace_1.2-4 dichromat_2.0-0 [10] digest_0.6.3 edgeR_3.4.0 evaluate_0.5.1 [13] formatR_0.10 genefilter_1.44.0 GenomicFeatures_1.14.2 [16] ggbio_1.10.7 ggplot2_0.9.3.1 GO.db_2.10.1 [19] GOstats_2.28.0 graph_1.40.0 grid_3.0.1 [22] gridExtra_0.9.1 GSEABase_1.24.0 gtable_0.1.2 [25] Hmisc_3.12-2 hwriter_1.3 labeling_0.2 [28] lattice_0.20-24 limma_3.18.3 locfit_1.5-9.1 [31] MASS_7.3-29 Matrix_1.1-0 munsell_0.4.2 [34] PFAM.db_2.10.1 plyr_1.8 proto_0.3-10 [37] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 [40] reshape2_1.2.2 R.methodsS3_1.5.2 R.oo_1.15.8 [43] rpart_4.1-3 Rsamtools_1.14.1 rtracklayer_1.22.0 [46] R.utils_1.28.4 scales_0.2.3 splines_3.0.1 [49] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 [52] tools_3.0.1 VariantAnnotation_1.8.5 XML_3.98-1.1 [55] xtable_1.7-1 zlibbioc_1.8.0 Thank you and best regards. ----- Amandine Fournier Lyon Neuroscience Research Center & Lyon Civil Hospital (France)
GO BSgenome BSgenome ReportingTools DESeq2 GO BSgenome BSgenome ReportingTools DESeq2 • 1.1k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Amandine, This warning just means that the ReportingTools package is relying on a function that has been deprecated, where deprecated means that the function still works correctly for now, but in the next version of Bioconductor it will not. There isn't anything for you to do; this warning is really something that the maintainer of ReportingTools needs to correct prior to the release of BioC 2.14 in April. Best, Jim On Thursday, November 21, 2013 10:58:10 AM, amandine.fournier at chu-lyon.fr wrote: > > Hi, > > I am currently using the last version of the DESeq2 package to analyse some RNA-Seq data. I would like to use the ReportingTools package to export the results, but I am facing a warning. > > My code is : > >> library("DESeq2") >> sampleFiles = c("htseqcount_Sample_1.txt","htseqcount_Sample_2.txt" ,"htseqcount_Sample_3.txt","htseqcount_Sample_4.txt") >> sampleCondition = c("case","control","case","control") >> sampleNames = c("Sample_1","Sample_2","Sample_3","Sample_4") >> sampleTable <- data.frame(sampleName = sampleNames, fileName = sampleFiles, condition = sampleCondition) >> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = "./", design = ~ condition) >> colData(dds)$condition = factor(colData(dds)$condition, levels = c("control","case")) >> dds <- DESeq(dds) >> res <- results(dds) > >> library(ReportingTools) >> library("BSgenome.Hsapiens.UCSC.hg19") >> des2Report <- HTMLReport(shortName='RNAseq_analysis_with_DESeq2', title='RNA-seq analysis of differential expression', reportDirectory="./reports") >> publish(dds, des2Report, pvalueCutoff=0.05, annotation.db="BSgenome.Hsapiens.UCSC.hg19", factor = colData(dds)$conditions, reportDir="./reports") > > Message d'avis : > In cols(db) : > 'cols' has been deprecated and replaced by 'columns' for versions of > Bioc that are higher than 2.13. Please use 'columns' anywhere that > you previously used 'cols' > > Does anybody known what is wrong and how to fix it ? > > Here is my sessionInfo() : > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C > [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 > [5] LC_MONETARY=fr_FR.utf8 LC_MESSAGES=fr_FR.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0 > [3] Biostrings_2.30.1 ReportingTools_2.2.0 > [5] AnnotationDbi_1.24.0 Biobase_2.22.0 > [7] RSQLite_0.11.4 DBI_0.2-7 > [9] knitr_1.5 DESeq2_1.2.5 > [11] RcppArmadillo_0.3.920.3 Rcpp_0.10.6 > [13] GenomicRanges_1.14.3 XVector_0.2.0 > [15] IRanges_1.20.5 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationForge_1.4.4 biomaRt_2.18.0 > [4] biovizBase_1.10.3 bitops_1.0-6 Category_2.28.0 > [7] cluster_1.14.4 colorspace_1.2-4 dichromat_2.0-0 > [10] digest_0.6.3 edgeR_3.4.0 evaluate_0.5.1 > [13] formatR_0.10 genefilter_1.44.0 GenomicFeatures_1.14.2 > [16] ggbio_1.10.7 ggplot2_0.9.3.1 GO.db_2.10.1 > [19] GOstats_2.28.0 graph_1.40.0 grid_3.0.1 > [22] gridExtra_0.9.1 GSEABase_1.24.0 gtable_0.1.2 > [25] Hmisc_3.12-2 hwriter_1.3 labeling_0.2 > [28] lattice_0.20-24 limma_3.18.3 locfit_1.5-9.1 > [31] MASS_7.3-29 Matrix_1.1-0 munsell_0.4.2 > [34] PFAM.db_2.10.1 plyr_1.8 proto_0.3-10 > [37] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [40] reshape2_1.2.2 R.methodsS3_1.5.2 R.oo_1.15.8 > [43] rpart_4.1-3 Rsamtools_1.14.1 rtracklayer_1.22.0 > [46] R.utils_1.28.4 scales_0.2.3 splines_3.0.1 > [49] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 > [52] tools_3.0.1 VariantAnnotation_1.8.5 XML_3.98-1.1 > [55] xtable_1.7-1 zlibbioc_1.8.0 > > > Thank you and best regards. > > ----- > Amandine Fournier > Lyon Neuroscience Research Center > & Lyon Civil Hospital (France) > _______________________________________________ > 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 -- 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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Hi Amandine, Jim is correct. We were using a deprecated parameter for annotating genes. The current dev version (2.3.3) should no longer throw that warning. Thanks, Jason On Nov 21, 2013, at 8:11 AM, James W. MacDonald wrote: > Hi Amandine, > > This warning just means that the ReportingTools package is relying on a function that has been deprecated, where deprecated means that the function still works correctly for now, but in the next version of Bioconductor it will not. > > There isn't anything for you to do; this warning is really something that the maintainer of ReportingTools needs to correct prior to the release of BioC 2.14 in April. > > Best, > > Jim > > > > On Thursday, November 21, 2013 10:58:10 AM, amandine.fournier@chu- lyon.fr wrote: >> >> Hi, >> >> I am currently using the last version of the DESeq2 package to analyse some RNA-Seq data. I would like to use the ReportingTools package to export the results, but I am facing a warning. >> >> My code is : >> >>> library("DESeq2") >>> sampleFiles = c("htseqcount_Sample_1.txt","htseqcount_Sample_2.txt ","htseqcount_Sample_3.txt","htseqcount_Sample_4.txt") >>> sampleCondition = c("case","control","case","control") >>> sampleNames = c("Sample_1","Sample_2","Sample_3","Sample_4") >>> sampleTable <- data.frame(sampleName = sampleNames, fileName = sampleFiles, condition = sampleCondition) >>> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = "./", design = ~ condition) >>> colData(dds)$condition = factor(colData(dds)$condition, levels = c("control","case")) >>> dds <- DESeq(dds) >>> res <- results(dds) >> >>> library(ReportingTools) >>> library("BSgenome.Hsapiens.UCSC.hg19") >>> des2Report <- HTMLReport(shortName='RNAseq_analysis_with_DESeq2', title='RNA-seq analysis of differential expression', reportDirectory="./reports") >>> publish(dds, des2Report, pvalueCutoff=0.05, annotation.db="BSgenome.Hsapiens.UCSC.hg19", factor = colData(dds)$conditions, reportDir="./reports") >> >> Message d'avis : >> In cols(db) : >> 'cols' has been deprecated and replaced by 'columns' for versions of >> Bioc that are higher than 2.13. Please use 'columns' anywhere that >> you previously used 'cols' >> >> Does anybody known what is wrong and how to fix it ? >> >> Here is my sessionInfo() : >> >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C >> [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 >> [5] LC_MONETARY=fr_FR.utf8 LC_MESSAGES=fr_FR.utf8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0 >> [3] Biostrings_2.30.1 ReportingTools_2.2.0 >> [5] AnnotationDbi_1.24.0 Biobase_2.22.0 >> [7] RSQLite_0.11.4 DBI_0.2-7 >> [9] knitr_1.5 DESeq2_1.2.5 >> [11] RcppArmadillo_0.3.920.3 Rcpp_0.10.6 >> [13] GenomicRanges_1.14.3 XVector_0.2.0 >> [15] IRanges_1.20.5 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.40.0 AnnotationForge_1.4.4 biomaRt_2.18.0 >> [4] biovizBase_1.10.3 bitops_1.0-6 Category_2.28.0 >> [7] cluster_1.14.4 colorspace_1.2-4 dichromat_2.0-0 >> [10] digest_0.6.3 edgeR_3.4.0 evaluate_0.5.1 >> [13] formatR_0.10 genefilter_1.44.0 GenomicFeatures_1.14.2 >> [16] ggbio_1.10.7 ggplot2_0.9.3.1 GO.db_2.10.1 >> [19] GOstats_2.28.0 graph_1.40.0 grid_3.0.1 >> [22] gridExtra_0.9.1 GSEABase_1.24.0 gtable_0.1.2 >> [25] Hmisc_3.12-2 hwriter_1.3 labeling_0.2 >> [28] lattice_0.20-24 limma_3.18.3 locfit_1.5-9.1 >> [31] MASS_7.3-29 Matrix_1.1-0 munsell_0.4.2 >> [34] PFAM.db_2.10.1 plyr_1.8 proto_0.3-10 >> [37] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [40] reshape2_1.2.2 R.methodsS3_1.5.2 R.oo_1.15.8 >> [43] rpart_4.1-3 Rsamtools_1.14.1 rtracklayer_1.22.0 >> [46] R.utils_1.28.4 scales_0.2.3 splines_3.0.1 >> [49] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 >> [52] tools_3.0.1 VariantAnnotation_1.8.5 XML_3.98-1.1 >> [55] xtable_1.7-1 zlibbioc_1.8.0 >> >> >> Thank you and best regards. >> >> ----- >> Amandine Fournier >> Lyon Neuroscience Research Center >> & Lyon Civil Hospital (France) >> _______________________________________________ >> 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 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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Jason A. Hackney, Ph.D. Bioinformatics and Computational Biology Genentech, Inc. hackney.jason@gene.com 650-467-5084 [[alternative HTML version deleted]]
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