[BioC] Question about ReportingTools used with DESeq2

James W. MacDonald jmacdon at uw.edu
Thu Nov 21 17:11:24 CET 2013


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)
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--
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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