[Bioc-devel] error using the DEXSeqDataSet function
Leonard Goldstein
goldstein.leonard at gene.com
Thu Jul 30 19:00:20 CEST 2015
Dear Alejandro,
DEXSeq is working fine now. Thanks very much for the quick fix.
Best wishes,
Leonard
On Thu, Jul 30, 2015 at 9:02 AM, Alejandro Reyes
<alejandro.reyes at embl.de> wrote:
> 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:
>
>> 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(),
>
>> 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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