jarod_v6 at libero.it
2014-Nov-16 18:25 UTC
[R] Problem on annotation of Deseq2 on reportingtools
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
[[alternative HTML version deleted]]
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]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793