[BioC] TCC RNAseq normalization package error

Asela Wijeratne [guest] guest at bioconductor.org
Thu Aug 22 23:21:59 CEST 2013

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)

 [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            

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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