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

The problem might be that your package versions are not consistent.

Bioc 2.14 had DESeq2 v1.4 and ReportingTools v2.4

Bioc 3.0 (current release) has DESeq2 v1.6 and ReportingTools v2.6

You have: DESeq2 v1.4 and ReportingTools v2.2

Try updating ReportingTools with biocLite("ReportingTools"), and then you might also try updating Bioconductor to the current release (because if there did happen to be a bug, developers can only push fixes to the release or devel branches, not to past versions of Bioc).

I'm not exactly sure what the proper syntax should be for the hand off... but I'd recommend building the results table with DESeq2's results() function, then passing the results table, which is a DESeqResults object, to ReportingTools. This is supported by ReportingTools, and this way, the DESeq2 ?results documentation is right at hand. See ReportingTools ?publish for the DESeqResults method.

Jarod,

I spoke with my co-maintainer (Jason Hackney) who understands the specific bio-related methods much better than I do and he suspects that Michael is correct that the issue arrises from a version mismatch between ReportingTools and DESeq2.

Did updating as Michael suggested solve your problem?

~G