[BioC] TCC RNAseq normalization package error
Ryan C. Thompson
rct at thompsonclan.org
Fri Aug 23 00:39:26 CEST 2013
The edgeR package also has a function called "calcNormFactors", and I
believe that they take different arguments. You may have to explicitly
specify the TCC function using "TCC::calcNormFactors".
On Thu 22 Aug 2013 02:21:59 PM PDT, Asela Wijeratne [guest] wrote:
>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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