[Bioc-devel] error using the DEXSeqDataSet function

[Leonard Goldstein]

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
>