[BioC] Question about ReportingTools used with DESeq2

amandine.fournier at chu-lyon.fr amandine.fournier at chu-lyon.fr
Thu Nov 21 16:58:10 CET 2013


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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