[R] Problem on annotation of Deseq2 on reportingtools

[jarod_v6 at libero.it]

Dear all!,

I use this code:


dds <- DESeq(ddHTSeq)
res <-results(dds)
#reporting
library(ReportingTools)
library("org.Hs.eg.db")
des2Report <- HTMLReport(shortName ='RNAseq_analysis_DESeq2.html',title ='RNA-seq analysis of differential expression using DESeq2 ',reportDirectory = "./Reports")
#publish(dds,des2Report,pvalueCutoff=0.05,annotation.db="org,Hs.eg.db")
publish(dds,des2Report,pvalueCutoff=0.01,annotation.db="org.Hs.egENSEMBL2EG",factor=colData(dds)$condition,categorySize=5)
finish(des2Report) 

and I have this error:
Error in results(object, resultName) : 
  'contrast', as a character vector of length 3, should have the form:
contrast = c('factorName','numeratorLevel','denominatorLevel'),
see the manual page of ?results for more information


is.factor(colData(dds)$condition)
[1] TRUE
> 
What can I do?


 sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pvclust_1.2-2             gplots_2.13.0             genefilter_1.44.0        
 [4] ReportingTools_2.2.0      knitr_1.6                 org.Hs.eg.db_2.10.1      
 [7] RSQLite_0.11.4            DBI_0.2-7                 annotate_1.40.1          
[10] AnnotationDbi_1.24.0      Biobase_2.22.0            biomaRt_2.18.0           
[13] DESeq2_1.4.5              RcppArmadillo_0.4.300.8.0 Rcpp_0.11.2              
[16] GenomicRanges_1.14.4      XVector_0.2.0             IRanges_1.20.7           
[19] BiocGenerics_0.8.0       

loaded via a namespace (and not attached):
 [1] AnnotationForge_1.4.4    Biostrings_2.30.1        biovizBase_1.10.8       
 [4] bitops_1.0-6             BSgenome_1.30.0          Category_2.28.0         
 [7] caTools_1.17             cluster_1.15.3           colorspace_1.2-4        
[10] dichromat_2.0-0          digest_0.6.4             edgeR_3.4.2             
[13] evaluate_0.5.5           formatR_0.10             Formula_1.1-1           
[16] gdata_2.13.3             geneplotter_1.40.0       GenomicFeatures_1.14.5  
[19] ggbio_1.10.16            ggplot2_1.0.0            GO.db_2.10.1            
[22] GOstats_2.28.0           graph_1.40.1             grid_3.1.1              
[25] gridExtra_0.9.1          GSEABase_1.24.0          gtable_0.1.2            
[28] gtools_3.4.1             Hmisc_3.14-4             hwriter_1.3             
[31] KernSmooth_2.23-13       lattice_0.20-29          latticeExtra_0.6-26     
[34] limma_3.18.13            locfit_1.5-9.1           MASS_7.3-34             
[37] Matrix_1.1-4             munsell_0.4.2            PFAM.db_2.10.1          
[40] plyr_1.8.1               proto_0.3-10             RBGL_1.38.0             
[43] RColorBrewer_1.0-5       RCurl_1.95-4.1           reshape2_1.4            
[46] R.methodsS3_1.6.1        R.oo_1.18.0              Rsamtools_1.14.3        
[49] rtracklayer_1.22.7       R.utils_1.32.4           scales_0.2.4            
[52] splines_3.1.1            stats4_3.1.1             stringr_0.6.2           
[55] survival_2.37-7          tools_3.1.1              VariantAnnotation_1.8.13
[58] XML_3.98-1.1             xtable_1.7-3             zlibbioc_1.8.0

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