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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel