[BioC] TCC RNAseq normalization package error
Asela Wijeratne [guest]
guest at bioconductor.org
Thu Aug 22 23:21:59 CEST 2013
Hi,
I am trying to use TCC package to normalize RNAseq data. When I tried to use "calcNormFactors" fucntion with the demo data, it gives the following error:
> tcc <- calcNormFactors(tcc, norm.method = "tmm", test.method = "edger",
+ iteration = 3, FDR = 0.1, floorPDEG = 0.05)
Error in calcNormFactors(tcc, norm.method = "tmm", test.method = "edger", :
unused argument(s) (norm.method = "tmm", test.method = "edger", iteration = 3, FDR = 0.1, floorPDEG = 0.05)
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq_1.10.1 lattice_0.20-13 edgeR_3.2.3 limma_3.16.5 TCC_1.1.99 locfit_1.5-9.1 Biobase_2.18.0
[8] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] annotate_1.36.0 AnnotationDbi_1.20.7 baySeq_1.12.0 DBI_0.2-7 DESeq2_1.1.0 genefilter_1.40.0 geneplotter_1.36.0
[8] GenomicRanges_1.10.7 grid_2.15.2 IRanges_1.16.6 parallel_2.15.2 RColorBrewer_1.0-5 ROC_1.34.0 RSQLite_0.11.4
[15] splines_2.15.2 stats4_2.15.2 survival_2.37-2 tools_2.15.2 XML_3.95-0.1 xtable_1.7-1
--
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