Hi all, I'm seeing a bit of an unusually error that I've never come across before - hoping for some assistance.
I quantified pair-end RNA seq data using Salmon, loaded it into RStudio via tximeta and continued with the general Bioconductor DESeq2 pipeline structure. Everything is working as expected. However, when I ask one of my project students to rerun the analysis but on their machine, we run into the error:
gse <- summarizeToGene(se)
loading existing EnsDb created: 2020-09-21 10:50:18
obtaining transcript-to-gene mapping from database
loading existing gene ranges created: 2020-09-21 10:56:56
summarizing abundance
summarizing counts
summarizing length
Error in abundanceMatTx * lengthMatTx :
non-numeric argument to binary operator
I've never come across this error before. From the face of things, R is complaining that a non-numeric value eg. a name of something is being passed into a binary operator e.g., "+". I'm having the student double check the meta-data that makes up the prior call to se <- tximeta(colDataDF). However, one thought that came to mind were the quant.sf files generated by Salmon.
Due to Covid lockdown we're having to do all of this remotely and sadly the project student doesn't have the band width at home to download the RNA seq data and process the reads using Salmon. Therefore, he copied across my quantified .sf files instead, a fraction of the size.
Update: I've just updated my version of tximeta, so we both have 1.7.14. There are quite a few changes in the object attributes returned by summarizeToGene, however, my machine, can still process summarizeToGene() without throwing an error. I'm a little lost.
Also, I can successfully run both tximport::summarizeToGene() and tximeta::summarizeToGene(). The other machine is throwing the same error for both.
This is my R setup.
SessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] KEGGgraph_1.49.1 gprofiler2_0.2.0 ReportingTools_2.29.0
[4] knitr_1.29 org.Hs.eg.db_3.11.4 AnnotationDbi_1.51.3
[7] RColorBrewer_1.1-2 pheatmap_1.0.12 genefilter_1.71.0
[10] magrittr_1.5 dplyr_1.0.1 GGally_2.0.0
[13] tidyr_1.1.2 broom_0.7.0 ggplot2_3.3.2
[16] vsn_3.57.0 DESeq2_1.29.13 tximeta_1.7.14
[19] SummarizedExperiment_1.19.6 DelayedArray_0.15.4 matrixStats_0.56.0
[22] Matrix_1.2-18 Biobase_2.49.0 GenomicRanges_1.41.5
[25] GenomeInfoDb_1.25.10 IRanges_2.23.10 S4Vectors_0.27.12
[28] BiocGenerics_0.35.4
loaded via a namespace (and not attached):
[1] backports_1.1.10 GOstats_2.55.0 Hmisc_4.4-1
[4] AnnotationHub_2.21.5 BiocFileCache_1.13.1 plyr_1.8.6
[7] lazyeval_0.2.2 GSEABase_1.51.1 splines_4.0.2
[10] BiocParallel_1.23.2 digest_0.6.25 ensembldb_2.13.1
[13] htmltools_0.5.0 GO.db_3.11.4 checkmate_2.0.0
[16] memoise_1.1.0 BSgenome_1.57.6 cluster_2.1.0
[19] limma_3.45.14 Biostrings_2.57.2 annotate_1.67.1
[22] R.utils_2.10.1 ggbio_1.37.0 askpass_1.1
[25] prettyunits_1.1.1 jpeg_0.1-8.1 colorspace_1.4-1
[28] blob_1.2.1 rappdirs_0.3.1 xfun_0.16
[31] crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.1
[34] tximport_1.17.6 graph_1.67.1 VariantAnnotation_1.35.3
[37] survival_3.2-3 glue_1.4.1 gtable_0.3.0
[40] zlibbioc_1.35.0 XVector_0.29.3 Rgraphviz_2.33.0
[43] scales_1.1.1 DBI_1.1.0 edgeR_3.31.4
[46] Rcpp_1.0.5 viridisLite_0.3.0 xtable_1.8-4
[49] progress_1.2.2 htmlTable_2.1.0 foreign_0.8-80
[52] bit_4.0.4 OrganismDbi_1.31.0 preprocessCore_1.51.0
[55] Formula_1.2-3 AnnotationForge_1.31.2 htmlwidgets_1.5.1
[58] httr_1.4.2 ellipsis_0.3.1 R.methodsS3_1.8.1
[61] pkgconfig_2.0.3 reshape_0.8.8 XML_3.99-0.5
[64] nnet_7.3-14 dbplyr_1.4.4 locfit_1.5-9.4
[67] tidyselect_1.1.0 rlang_0.4.7 reshape2_1.4.4
[70] later_1.1.0.1 munsell_0.5.0 BiocVersion_3.12.0
[73] tools_4.0.2 generics_0.0.2 RSQLite_2.2.0
[76] stringr_1.4.0 fastmap_1.0.1 yaml_2.2.1
[79] bit64_4.0.5 purrr_0.3.4 AnnotationFilter_1.13.0
[82] RBGL_1.65.0 mime_0.9 R.oo_1.24.0
[85] biomaRt_2.45.2 compiler_4.0.2 rstudioapi_0.11
[88] plotly_4.9.2.1 curl_4.3 png_0.1-7
[91] interactiveDisplayBase_1.27.5 affyio_1.59.0 PFAM.db_3.11.4
[94] tibble_3.0.3 geneplotter_1.67.0 stringi_1.5.3
[97] GenomicFeatures_1.41.3 lattice_0.20-41 ProtGenerics_1.21.0
[100] vctrs_0.3.2 pillar_1.4.6 lifecycle_0.2.0
[103] BiocManager_1.30.10 data.table_1.13.0 bitops_1.0-6
[106] httpuv_1.5.4 rtracklayer_1.49.5 hwriter_1.3.2
[109] R6_2.4.1 latticeExtra_0.6-29 affy_1.67.0
[112] promises_1.1.1 gridExtra_2.3 dichromat_2.0-0
[115] assertthat_0.2.1 openssl_1.4.3 Category_2.55.0
[118] withr_2.2.0 GenomicAlignments_1.25.3 Rsamtools_2.5.3
[121] GenomeInfoDbData_1.2.3 hms_0.5.3 grid_4.0.2
[124] rpart_4.1-15 biovizBase_1.37.0 shiny_1.5.0
[127] base64enc_0.1-3
This is the setup that fails to generate a summarizeToGene result:
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] tximeta_1.7.14 tximport_1.17.6 SummarizedExperiment_1.19.6
[4] DelayedArray_0.15.8 matrixStats_0.56.0 Matrix_1.2-18
[7] Biobase_2.49.1 GenomicRanges_1.41.6 GenomeInfoDb_1.25.11
[10] IRanges_2.23.10 S4Vectors_0.27.13 BiocGenerics_0.35.4
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.1 bit64_4.0.5
[4] AnnotationHub_2.21.5 shiny_1.5.0 assertthat_0.2.1
[7] askpass_1.1 interactiveDisplayBase_1.27.5 BiocManager_1.30.10
[10] BiocFileCache_1.13.1 blob_1.2.1 Rsamtools_2.5.3
[13] GenomeInfoDbData_1.2.3 yaml_2.2.1 progress_1.2.2
[16] BiocVersion_3.12.0 pillar_1.4.6 RSQLite_2.2.0
[19] lattice_0.20-41 glue_1.4.2 digest_0.6.25
[22] promises_1.1.1 XVector_0.29.3 htmltools_0.5.0
[25] httpuv_1.5.4 XML_3.99-0.5 pkgconfig_2.0.3
[28] biomaRt_2.45.2 zlibbioc_1.35.0 purrr_0.3.4
[31] xtable_1.8-4 later_1.1.0.1 BiocParallel_1.23.2
[34] tibble_3.0.3 openssl_1.4.3 AnnotationFilter_1.13.0
[37] generics_0.0.2 ellipsis_0.3.1 GenomicFeatures_1.41.3
[40] lazyeval_0.2.2 magrittr_1.5 crayon_1.3.4
[43] mime_0.9 memoise_1.1.0 evaluate_0.14
[46] tools_4.0.2 prettyunits_1.1.1 hms_0.5.3
[49] lifecycle_0.2.0 stringr_1.4.0 ensembldb_2.13.1
[52] AnnotationDbi_1.51.3 Biostrings_2.57.2 compiler_4.0.2
[55] tinytex_0.25 rlang_0.4.7 grid_4.0.2
[58] RCurl_1.98-1.2 rstudioapi_0.11 rappdirs_0.3.1
[61] bitops_1.0-6 rmarkdown_2.3 DBI_1.1.0
[64] curl_4.3 R6_2.4.1 GenomicAlignments_1.25.3
[67] rtracklayer_1.49.5 knitr_1.29 dplyr_1.0.2
[70] fastmap_1.0.1 bit_4.0.4 ProtGenerics_1.21.0
[73] stringi_1.5.3 Rcpp_1.0.5 vctrs_0.3.4
[76] dbplyr_1.4.4 tidyselect_1.1.0 xfun_0.17
I suggest to ask this over at support.bioconductor.org where the package maintainers are more active than here. Be sure to provide a reproducible example if possible.