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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor