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       

hi Jo,

Thanks for the note. I will fix this in devel.

A workaround is to use estimateSizeFactorForMatrix() with a one row matrix and then sizeFactors(dds)<-