Entering edit mode
I've been trying to use DEXSeq to test for differential exon usage; it seems to run fine up to testForDEU until I get to fold changes.
mydex <- DEXSeq::estimateExonFoldChanges(mydex, fitExpToVar="cell")
Error in exp(alleffects) : non-numeric argument to mathematical function
I'm on R 3.6.1; freshly installed verion of DEXSeq this morning.
sessionInfo() below:
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.20-38 dplyr_0.8.3 purrr_0.3.3 SGSeq_1.20.0 Rsamtools_2.2.1
[6] Biostrings_2.54.0 XVector_0.26.0 GGally_1.4.0 ggplot2_3.2.1 data.table_1.12.6
[11] DEXSeq_1.32.0 RColorBrewer_1.1-2 AnnotationDbi_1.48.0 DESeq2_1.26.0 SummarizedExperiment_1.16.0
[16] DelayedArray_0.12.0 matrixStats_0.55.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 IRanges_2.20.1
[21] S4Vectors_0.24.0 Biobase_2.46.0 BiocGenerics_0.32.0 BiocParallel_1.20.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 bit64_0.9-7 progress_1.2.2 httr_1.4.1 tools_3.6.1
[6] backports_1.1.5 R6_2.4.1 rpart_4.1-15 Hmisc_4.3-0 DBI_1.0.0
[11] lazyeval_0.2.2 colorspace_1.4-1 nnet_7.3-12 withr_2.1.2 tidyselect_0.2.5
[16] gridExtra_2.3 prettyunits_1.0.2 bit_1.1-14 curl_4.2 compiler_3.6.1
[21] htmlTable_1.13.2 rtracklayer_1.46.0 labeling_0.3 scales_1.1.0 checkmate_1.9.4
[26] genefilter_1.68.0 askpass_1.1 rappdirs_0.3.1 stringr_1.4.0 digest_0.6.23
[31] foreign_0.8-72 base64enc_0.1-3 pkgconfig_2.0.3 htmltools_0.4.0 dbplyr_1.4.2
[36] htmlwidgets_1.5.1 rlang_0.4.2 rstudioapi_0.10 RSQLite_2.1.2 hwriter_1.3.2
[41] acepack_1.4.1 RCurl_1.95-4.12 magrittr_1.5 GenomeInfoDbData_1.2.2 Formula_1.2-3
[46] Matrix_1.2-17 Rcpp_1.0.3 munsell_0.5.0 stringi_1.4.3 zlibbioc_1.32.0
[51] plyr_1.8.4 BiocFileCache_1.10.2 grid_3.6.1 blob_1.2.0 crayon_1.3.4
[56] splines_3.6.1 GenomicFeatures_1.38.0 annotate_1.64.0 hms_0.5.2 locfit_1.5-9.1
[61] zeallot_0.1.0 knitr_1.26 pillar_1.4.2 igraph_1.2.4.1 RUnit_0.4.32
[66] reshape2_1.4.3 geneplotter_1.64.0 biomaRt_2.42.0 XML_3.98-1.20 glue_1.3.1
[71] latticeExtra_0.6-28 BiocManager_1.30.10 vctrs_0.2.0 gtable_0.3.0 openssl_1.4.1
[76] reshape_0.8.8 assertthat_0.2.1 xfun_0.11 xtable_1.8-4 survival_3.1-7
[81] tibble_2.1.3 GenomicAlignments_1.22.1 memoise_1.1.0 cluster_2.1.0 statmod_1.4.32
Thanks for reporting this. Do you have a reproducible example with data that I could use to debug?