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]]

