error in DEXSeq estimateExonFoldChanges
0
0
Entering edit mode
@brownannaleigh-22443
Last seen 4.3 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

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  
dexseq • 547 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 685 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6