[Bioc-devel] error using the DEXSeqDataSet function

Dear Leonard,

Thanks a lot for reporting this. It should be fixed in the version that 
I just committed to the svn (DEXSeq 1.5.10).

While debugging the DEXSeq code, I noticed that summarizedOverlaps is 
giving me an error, which I think its a bug while creating the 
summarizedExperiments object that is returned. Here a reproducible example:

Konsole output

   library(GenomicRanges)

>   library(GenomicFeatures)
 >   library(GenomicAlignments)
 >
 >   hse <- makeTxDbFromBiomart( biomart="ensembl",
+                               dataset="hsapiens_gene_ensembl" )


Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
 >
 >   bamDir <- system.file(
+     "extdata", package="parathyroidSE", mustWork=TRUE )
 >   fls <- list.files( bamDir, pattern="bam$", full=TRUE )
 >
 >   bamlst <- BamFileList(
+     fls, index=character(),
+     yieldSize=100000, obeyQname=TRUE )
 >
 >   exonicParts <- disjointExons( hse, aggregateGenes=FALSE )
 >
 >   SE <- summarizeOverlaps( exonicParts, bamlst,
+     mode="Union", singleEnd=FALSE,
+     ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE )
Error in SummarizedExperiment(assays = SimpleList(counts = counts), 
rowRanges = features,  :
  error in evaluating the argument 'assays' in selecting a method for 
function 'SummarizedExperiment': Error in validObject(.Object) :
  invalid class ?SimpleList? object: invalid object for slot "listData" 
in class "SimpleList": got class "matrix", should be or extend class "lis
t"

And the output of sessionInfo(),

Konsole output

 sessionInfo()

R Under development (unstable) (2015-07-25 r68744)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

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

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

other attached packages:
[1] GenomicAlignments_1.5.12   Rsamtools_1.21.14
[3] Biostrings_2.37.2          XVector_0.9.1
[5] GenomicFeatures_1.21.13    AnnotationDbi_1.31.17
[7] DEXSeq_1.15.10             DESeq2_1.9.26
[9] RcppArmadillo_0.5.200.1.0  Rcpp_0.12.0
[11] SummarizedExperiment_0.3.2 GenomicRanges_1.21.17
[13] GenomeInfoDb_1.5.9         IRanges_2.3.15
[15] S4Vectors_0.7.10           Biobase_2.29.1
[17] BiocGenerics_0.15.3        BiocParallel_1.3.42

loaded via a namespace (and not attached):
[1] genefilter_1.51.0    statmod_1.4.21       locfit_1.5-9.1
[4] reshape2_1.4.1       splines_3.3.0        lattice_0.20-33
[7] colorspace_1.2-6     rtracklayer_1.29.12  survival_2.38-3
[10] XML_3.98-1.3         foreign_0.8-65       DBI_0.3.1
[13] RColorBrewer_1.1-2   lambda.r_1.1.7       plyr_1.8.3
[16] stringr_1.0.0        zlibbioc_1.15.0      munsell_0.4.2
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2
[22] latticeExtra_0.6-26  geneplotter_1.47.0   biomaRt_2.25.1
[25] proto_0.3-10         acepack_1.3-3.3      xtable_1.7-4
[28] scales_0.2.5         Hmisc_3.16-0         annotate_1.47.4
[31] gridExtra_2.0.0      ggplot2_1.0.1        digest_0.6.8
[34] stringi_0.5-5        grid_3.3.0           tools_3.3.0
[37] bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7
[40] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3
[43] futile.options_1.0.0 MASS_7.3-43          rpart_4.1-10
[46] nnet_7.3-10


Best regards,
Alejandro Reyes

Hi all,

I'm having trouble creating a DEXSeqDataSet object (in the devel
version of DEXSeq)

Running the example included in the manual page results in the same
error I get with my own data (see below)

Many thanks for your help.

Leonard

library(DEXSeq)
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(

+     paste0("gene", 1:10),
+     each= 100 )

featureID <- rep(

+     paste0("exon", 1:10),
+     times= 100 )

DEXSeqDataSet( countData, sampleData, design,

+             featureID, groupID )
converting counts to integer mode

Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) :
   replacement has 1 row, data has 0
In addition: Warning message:
In DESeqDataSet(se, design, ignoreRank = TRUE) :
   900 duplicate rownames were renamed by adding numbers

sessionInfo()

R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] DEXSeq_1.15.9              DESeq2_1.9.26
  [3] RcppArmadillo_0.5.200.1.0  Rcpp_0.12.0
  [5] SummarizedExperiment_0.3.2 GenomicRanges_1.21.17
  [7] GenomeInfoDb_1.5.9         IRanges_2.3.15
  [9] S4Vectors_0.7.10           Biobase_2.29.1
[11] BiocGenerics_0.15.3        BiocParallel_1.3.41

loaded via a namespace (and not attached):
  [1] genefilter_1.51.0     statmod_1.4.21        locfit_1.5-9.1
  [4] reshape2_1.4.1        splines_3.2.1         lattice_0.20-33
  [7] colorspace_1.2-6      survival_2.38-3       XML_3.98-1.3
[10] foreign_0.8-65        DBI_0.3.1             RColorBrewer_1.1-2
[13] lambda.r_1.1.7        plyr_1.8.3            stringr_1.0.0
[16] zlibbioc_1.15.0       Biostrings_2.37.2     munsell_0.4.2
[19] gtable_0.1.2          futile.logger_1.4.1   hwriter_1.3.2
[22] latticeExtra_0.6-26   geneplotter_1.47.0    biomaRt_2.25.1
[25] AnnotationDbi_1.31.17 proto_0.3-10          acepack_1.3-3.3
[28] xtable_1.7-4          scales_0.2.5          Hmisc_3.16-0
[31] annotate_1.47.4       XVector_0.9.1         Rsamtools_1.21.14
[34] gridExtra_2.0.0       ggplot2_1.0.1         digest_0.6.8
[37] stringi_0.5-5         grid_3.2.1            tools_3.2.1
[40] bitops_1.0-6          magrittr_1.5          RCurl_1.95-4.7
[43] RSQLite_1.0.0         Formula_1.2-1         cluster_2.0.3
[46] futile.options_1.0.0  MASS_7.3-43           rpart_4.1-10
[49] compiler_3.2.1        nnet_7.3-10

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