[R] Problem on annotation of Deseq2 on reportingtools

[Martin Morgan]

On 11/16/2014 10:25 AM, jarod_v6 at libero.it wrote:
> 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?
>

Please ask questions about Bioconductor packages on the Bioconductor support site

   https://support.bioconductor.org

Martin
>
>   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
>
> 	[[alternative HTML version deleted]]
>
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