[Bioc-devel] error using the DEXSeqDataSet function
Alejandro Reyes
alejandro.reyes at embl.de
Thu Jul 30 18:02:24 CEST 2015
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
On 29.07.2015 20:26, Leonard Goldstein wrote:
> 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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