Hello,

First of all, thank you for developing and maintaining this great package.

I am trying to create DEXSeqDataSet by following the example from manual.

countData <- matrix( rpois(10000, 100), nrow=1000 )
sampleData <- data.frame(
condition=rep( c("untreated", "treated"), each=5 ) )
design <- formula( ~ sample + exon + condition:exon )
groupID <- rep(
sprintf("gene
each= 100 )
featureID <- rep(
sprintf("exon
times= 100 )
DEXSeqDataSet( countData, sampleData, design,
featureID, groupID )

There is something missing regarding to featureID and groupID.

For my code
library(DEXSeq)
library(parallel)
#newData <-
data[,c(which(Basal.index),which(Her2.index),which(LumA.index),which(LumB.index))]
condition =
c(rep('LumA',length(which(LumA.index))),rep('LumB',length(which(LumB.index))))
newData <- data[,c(which(LumA.index),which(LumB.index))]
newData <- sapply(newData, as.numeric)
# > dim(newData)
# [1] 224158    357
#cds = newExonCountSet(newData, condition, gene.ids, exon.ids )
design <- formula( ~ sample + exon + condition:exon )
sampleData = data.frame(condition)
rownames(sampleData) <- colnames(newData)
featureID = exon.ids
groupID = gene.ids
cds = DEXSeqDataSet(newData, sampleData,
                    design,
                    featureID, groupID)

But always receiving following error:
Error in .Method(..., deparse.level = deparse.level) :
  number of rows of matrices must match (see arg 2)

How can I fix this error?

Thank you for your assistance in advance.

Best,
Hatice

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] DEXSeq_1.10.0           BiocParallel_0.6.0      DESeq2_1.4.1
 [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1             GenomicRanges_1.16.1
 [7] GenomeInfoDb_1.0.2      IRanges_1.22.6          Biobase_2.24.0
[10] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] annotate_1.42.0      AnnotationDbi_1.26.0 BatchJobs_1.2
 [4] BBmisc_1.5           biomaRt_2.20.0       Biostrings_2.32.0
 [7] bitops_1.0-6         brew_1.0-6           codetools_0.2-8
[10] DBI_0.2-7            digest_0.6.4         fail_1.2
[13] foreach_1.4.2        genefilter_1.46.0    geneplotter_1.42.0
[16] grid_3.1.0           hwriter_1.3          iterators_1.0.7
[19] lattice_0.20-29      locfit_1.5-9.1       plyr_1.8.1
[22] RColorBrewer_1.0-5   RCurl_1.95-4.1       Rsamtools_1.16.0
[25] RSQLite_0.11.4       sendmailR_1.1-2      splines_3.1.0
[28] statmod_1.4.19       stats4_3.1.0         stringr_0.6.2
[31] survival_2.37-7      tools_3.1.0          XML_3.98-1.1
[34] xtable_1.7-3         XVector_0.4.0        zlibbioc_1.10.0

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