On 11/16/2014 10:25 AM, jarod...@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_0.11.4DBI_0.2-7 annotate_1.40.1
[10] AnnotationDbi_1.24.0 Biobase_2.22.0biomaRt_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_1.4.4Biostrings_2.30.1biovizBase_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_1.10.16ggplot2_1.0.0GO.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_3.18.13locfit_1.5-9.1 MASS_7.3-34
[37] Matrix_1.1-4 munsell_0.4.2PFAM.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_1.6.1R.oo_1.18.0 Rsamtools_1.14.3
[49] rtracklayer_1.22.7 R.utils_1.32.4 scales_0.2.4
[52] splines_3.1.1stats4_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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
