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]]