error in DEXSeq estimateExonFoldChanges
Entering edit mode
Last seen 3.0 years ago

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

[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  
dexseq • 358 views
Entering edit mode

Thanks for reporting this. Do you have a reproducible example with data that I could use to debug?


Login before adding your answer.

Traffic: 439 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6