[BioC] TCC RNAseq normalization package error

[Ryan C. Thompson]

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
>
> --
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>
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