Hi,
I am running DEXSeq (DEXSeq_1.12.2) and getting an error message, when trying to calculate the Exon fold-changes.
I have tried both the single commands-method as well as the DEXSeq
() wrapper. the script I am using as well as the sessionInfo
are added at the bottom.
In both cases ( for the wrapper I can only assume) I am getting the following error message when calculating the exon fold-changes
using supplied model matrix ... using supplied model matrix using supplied model matrix Error in exp(alleffects) : non-numeric argument to mathematical function
As the complete dataset is too big to run multiple times, I have created a subset with only the first 1000 genes, but it still gives me the error message.
Does it has anything to do with the sampleTable I am using?
> CR4W0h.CTRL0hsampleTable sampleName treatment replica timepoint condition 11 CR4Wo1 CR4Wo 1 0h CR4Wo0h 12 CR4Wo2 CR4Wo 2 0h CR4Wo0h 13 CR4Wo3 CR4Wo 3 0h CR4Wo0h 14 CR4Wo4 CR4Wo 4 0h CR4Wo0h 1 C20 ctrl 1 0h ctrl0h 2 C22 ctrl 2 0h ctrl0h 3 C23 ctrl 3 0h ctrl0h 4 C24 ctrl 4 0h ctrl0h
Thanks a lot for any help,
Assa
Here is my script:
# creating the DEXSeq object CR4W0h.CTRL0hdxd <- DEXSeqDataSetFromHTSeq(CR4W0h.CTRL0hfiles, + sampleData = CR4W0h.CTRL0hsampleTable, + design = ~sample + exon + treatment:exon, + flattenedfile = flattenedFile) # use the single command mode: CR4W0h.CTRL0hdxd = estimateSizeFactors( dxdtest ) CR4W0h.CTRL0hdxd = estimateDispersions( CR4W0h.CTRL0hdxd, BPPARAM=BPPARAM) CR4W0h.CTRL0hdxd = testForDEU( CR4W0h.CTRL0hdxd, BPPARAM=BPPARAM ) CR4W0h.CTRL0hdxd = estimateExonFoldChanges( CR4W0h.CTRL0hdxd, fitExpToVar="treatment", BPPARAM=BPPARAM) CR4W0h.CTRL0hdxr <- DEXSeqResults(object = CR4W0h.CTRL0hdxd)
# using the wrapper command CR4W0h.CTRL0hdxd <- DEXSeq(object = CR4W0h.CTRL0hdxd, fullModel = ~sample + exon + treatment:exon,BPPARAM = BPPARAM, fitExpToVar = "treatment" ) > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) 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] rtracklayer_1.26.3 DEXSeq_1.12.2 [3] BiocParallel_1.0.3 DESeq2_1.6.3 [5] RcppArmadillo_0.6.200.2.0 Rcpp_0.12.2 [7] GenomicRanges_1.18.4 GenomeInfoDb_1.2.5 [9] IRanges_2.0.1 S4Vectors_0.4.0 [11] Biobase_2.26.0 BiocGenerics_0.12.1 [13] BiocInstaller_1.16.5 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 annotate_1.44.0 AnnotationDbi_1.28.2 [4] base64enc_0.1-3 BatchJobs_1.6 BBmisc_1.9 [7] biomaRt_2.22.0 Biostrings_2.34.1 bitops_1.0-6 [10] brew_1.0-6 checkmate_1.6.3 cluster_2.0.3 [13] codetools_0.2-14 colorspace_1.2-6 DBI_0.3.1 [16] digest_0.6.8 fail_1.3 foreach_1.4.3 [19] foreign_0.8-66 Formula_1.2-1 genefilter_1.48.1 [22] geneplotter_1.44.0 GenomicAlignments_1.2.2 ggplot2_1.0.1 [25] grid_3.1.0 gridExtra_2.0.0 gtable_0.1.2 [28] Hmisc_3.17-0 hwriter_1.3.2 iterators_1.0.8 [31] lattice_0.20-33 latticeExtra_0.6-26 locfit_1.5-9.1 [34] magrittr_1.5 MASS_7.3-45 munsell_0.4.2 [37] nnet_7.3-11 plyr_1.8.3 proto_0.3-10 [40] RColorBrewer_1.1-2 RCurl_1.95-4.7 reshape2_1.4.1 [43] rpart_4.1-10 Rsamtools_1.18.3 RSQLite_1.0.0 [46] scales_0.3.0 sendmailR_1.2-1 splines_3.1.0 [49] statmod_1.4.22 stringi_1.0-1 stringr_1.0.0 [52] survival_2.38-3 tools_3.1.0 XML_3.98-1.3 [55] xtable_1.8-0 XVector_0.6.0 zlibbioc_1.12.0
interestingly it happens on the Ubuntu (14.04.3) server, but not on my iMac (which break down if I try to run the whole data set)
Hi Assa,
1. Could you try to update your R and Bioconductor to either the release version or the development version, and see if the error persists?
2. Can you include the sessionInfo() from your iMac?
Alejandro
I added the seesionInfo() from my iMac below
I am now updating the R vesrion on my server