Entering edit mode
dear all!
I recently experienced that it is not possible to normalize the counts of a miRNA-seq experiment using estimateSizeFactors
against a single normalization control. Below is the code and the error.
> NORM <- "hsa-miR-30a-5p" > idx <- which( rownames( Counts.deseq )==NORM ) > Counts.deseq.cnorm <- estimateSizeFactors( Counts.deseq, controlGenes=idx ) Error in apply(counts[controlGenes, ], 2, function(cnts) { : dim(X) must have a positive length
I suggest to add a drop=FALSE
to avoid that problem (i.e. counts[ controlGenes, , drop=FALSE ]
).
cheers, jo
my R-version etc:
> sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin14.0.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DESeq2_1.6.2 RcppArmadillo_0.4.550.1.0 [3] Rcpp_0.11.3 GenomicRanges_1.18.4 [5] GenomeInfoDb_1.2.4 IRanges_2.0.1 [7] S4Vectors_0.4.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 annotate_1.44.0 AnnotationDbi_1.28.1 [4] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 [7] Biobase_2.26.0 BiocParallel_1.0.0 brew_1.0-6 [10] checkmate_1.5.1 cluster_1.15.3 codetools_0.2-9 [13] colorspace_1.2-4 DBI_0.3.1 digest_0.6.8 [16] fail_1.2 foreach_1.4.2 foreign_0.8-62 [19] Formula_1.1-2 genefilter_1.48.1 geneplotter_1.44.0 [22] ggplot2_1.0.0 grid_3.1.2 gtable_0.1.2 [25] Hmisc_3.14-6 iterators_1.0.7 lattice_0.20-29 [28] latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-37 [31] munsell_0.4.2 nnet_7.3-8 plyr_1.8.1 [34] proto_0.3-10 RColorBrewer_1.1-2 reshape2_1.4.1 [37] rpart_4.1-8 RSQLite_1.0.0 scales_0.2.4 [40] sendmailR_1.2-1 splines_3.1.2 stringr_0.6.2 [43] survival_2.37-7 tools_3.1.2 XML_3.98-1.1 [46] xtable_1.7-4 XVector_0.6.0
thanks Micheal!