(Sorry, the formatting got messed up. here is the same post again, with proper formatting.)

Dear DEXSeq Developers,

I got tripped by some errors (in estimateSizeFactors and estimateExonFoldChanges functions) when working with a DEXSeqDataset object that is obtained by subsetting the columns (samples) of another DEXSeqDataset object.

I thought I would let you know of the error I got and how I fixed it, so that: 
1) you could tell me if this is indeed a proper way to subset columns? (for instance, I fix the error by subsetting object@modelFrameBM ; am I missing any other slots that need to be subsetted too?) 
2) as a feature request, could a simpler way to subset columns be included in future versions of DEXSeq, by doing the necessary modelFrameBM subsetting and droplevels() when the DEXSeqDataSet object is being subsetted? 

The full code is here and sessionInfo is in PS below.

> data(pasillaDEXSeqDataSet, package="pasilla")
> dxr = DEXSeq(dxd)
using supplied model matrix
using supplied model matrix
> dxdsub = dxd[,dxd$type=="paired-end"];  for (col in names(colData(dxdsub))) {  if (is.factor(dxdsub[[col]])) {  dxdsub[[col]] = droplevels(dxdsub[[col]]); }  }
> dxrsub = DEXSeq(dxdsub)
Error in `$<-.data.frame`(`*tmp*`, "sizeFactor", value = c(0.943530200961566,  : 
  replacement has 392 rows, data has 686
> dxdsub@modelFrameBM = {  mf=dxdsub@modelFrameBM; droplevels(mf[mf$type=="paired-end",])  }
> dxrsub = DEXSeq(dxdsub)
using supplied model matrix
using supplied model matrix

Thanks, 
Mani

PS: > sessionInfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.12.2             BiocParallel_1.0.3        DESeq2_1.6.3              RcppArmadillo_0.6.200.2.0 Rcpp_0.12.1               GenomicRanges_1.18.4      GenomeInfoDb_1.2.5        IRanges_2.0.1            
 [9] S4Vectors_0.4.0           Biobase_2.26.0            BiocGenerics_0.12.1       BiocInstaller_1.16.5     

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.44.0      AnnotationDbi_1.28.2 base64enc_0.1-3      BatchJobs_1.6        BBmisc_1.9           biomaRt_2.22.0       Biostrings_2.34.1    bitops_1.0-6         brew_1.0-6           checkmate_1.6.3     
[12] cluster_1.15.3       codetools_0.2-9      colorspace_1.2-6     DBI_0.3.1            digest_0.6.8         fail_1.3             foreach_1.4.3        foreign_0.8-61       Formula_1.2-1        genefilter_1.48.1    geneplotter_1.44.0  
[23] ggplot2_1.0.1        grid_3.1.2           gridExtra_2.0.0      gtable_0.1.2         Hmisc_3.17-0         hwriter_1.3.2        iterators_1.0.8      lattice_0.20-29      latticeExtra_0.6-26  locfit_1.5-9.1       magrittr_1.5        
[34] MASS_7.3-35          munsell_0.4.2        nnet_7.3-8           plyr_1.8.3           proto_0.3-10         RColorBrewer_1.1-2   RCurl_1.95-4.7       reshape2_1.4.1       rpart_4.1-8          Rsamtools_1.18.3     RSQLite_1.0.0       
[45] scales_0.3.0         sendmailR_1.2-1      splines_3.1.2        statmod_1.4.22       stringi_1.0-1        stringr_1.0.0        survival_2.37-7      tools_3.1.2          XML_3.98-1.3         xtable_1.8-0         XVector_0.6.0       
[56] zlibbioc_1.12.0