Hi all, I'm seeing a bit of an unusually error that I've never come across before - hoping for some assistance. I had posted to Biostars, recommendations were to put it up here.
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 on their machine, he runs 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 bandwidth at home to download the RNA seq data and process the reads using Salmon. Therefore, he's using the quantified .sf files I generated, a fraction of the size. My initial concern is some machine-dependent association with the quant.sf files.
I noticed we had different versions of tximeta, so I brought my version up to 1.7.14. There are quite a few changes in the object attributes returned by summarizeToGene between my original version of tximeta (1.7.4) and the later version, however, my machine, can still execute summarizeToGene() without throwing an error.
We tried using tximport as an alternative to tximeta. The tximport::summarizeToGene() yields a valid object on my machine, however, fails with a similar error to the one above on my students machine.
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:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252  LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  KEGGgraph_1.49.1 gprofiler2_0.2.0 ReportingTools_2.29.0  knitr_1.29 org.Hs.eg.db_3.11.4 AnnotationDbi_1.51.3  RColorBrewer_1.1-2 pheatmap_1.0.12 genefilter_1.71.0  magrittr_1.5 dplyr_1.0.1 GGally_2.0.0  tidyr_1.1.2 broom_0.7.0 ggplot2_3.3.2  vsn_3.57.0 DESeq2_1.29.13 tximeta_1.7.14  SummarizedExperiment_1.19.6 DelayedArray_0.15.4 matrixStats_0.56.0  Matrix_1.2-18 Biobase_2.49.0 GenomicRanges_1.41.5  GenomeInfoDb_1.25.10 IRanges_2.23.10 S4Vectors_0.27.12  BiocGenerics_0.35.4 loaded via a namespace (and not attached):  backports_1.1.10 GOstats_2.55.0 Hmisc_4.4-1  AnnotationHub_2.21.5 BiocFileCache_1.13.1 plyr_1.8.6  lazyeval_0.2.2 GSEABase_1.51.1 splines_4.0.2  BiocParallel_1.23.2 digest_0.6.25 ensembldb_2.13.1  htmltools_0.5.0 GO.db_3.11.4 checkmate_2.0.0  memoise_1.1.0 BSgenome_1.57.6 cluster_2.1.0  limma_3.45.14 Biostrings_2.57.2 annotate_1.67.1  R.utils_2.10.1 ggbio_1.37.0 askpass_1.1  prettyunits_1.1.1 jpeg_0.1-8.1 colorspace_1.4-1  blob_1.2.1 rappdirs_0.3.1 xfun_0.16  crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.1  tximport_1.17.6 graph_1.67.1 VariantAnnotation_1.35.3  survival_3.2-3 glue_1.4.1 gtable_0.3.0  zlibbioc_1.35.0 XVector_0.29.3 Rgraphviz_2.33.0  scales_1.1.1 DBI_1.1.0 edgeR_3.31.4  Rcpp_1.0.5 viridisLite_0.3.0 xtable_1.8-4  progress_1.2.2 htmlTable_2.1.0 foreign_0.8-80  bit_4.0.4 OrganismDbi_1.31.0 preprocessCore_1.51.0  Formula_1.2-3 AnnotationForge_1.31.2 htmlwidgets_1.5.1  httr_1.4.2 ellipsis_0.3.1 R.methodsS3_1.8.1  pkgconfig_2.0.3 reshape_0.8.8 XML_3.99-0.5  nnet_7.3-14 dbplyr_1.4.4 locfit_1.5-9.4  tidyselect_1.1.0 rlang_0.4.7 reshape2_1.4.4  later_22.214.171.124 munsell_0.5.0 BiocVersion_3.12.0  tools_4.0.2 generics_0.0.2 RSQLite_2.2.0  stringr_1.4.0 fastmap_1.0.1 yaml_2.2.1  bit64_4.0.5 purrr_0.3.4 AnnotationFilter_1.13.0  RBGL_1.65.0 mime_0.9 R.oo_1.24.0  biomaRt_2.45.2 compiler_4.0.2 rstudioapi_0.11  plotly_126.96.36.199 curl_4.3 png_0.1-7  interactiveDisplayBase_1.27.5 affyio_1.59.0 PFAM.db_3.11.4  tibble_3.0.3 geneplotter_1.67.0 stringi_1.5.3  GenomicFeatures_1.41.3 lattice_0.20-41 ProtGenerics_1.21.0  vctrs_0.3.2 pillar_1.4.6 lifecycle_0.2.0  BiocManager_1.30.10 data.table_1.13.0 bitops_1.0-6  httpuv_1.5.4 rtracklayer_1.49.5 hwriter_1.3.2  R6_2.4.1 latticeExtra_0.6-29 affy_1.67.0  promises_1.1.1 gridExtra_2.3 dichromat_2.0-0  assertthat_0.2.1 openssl_1.4.3 Category_2.55.0  withr_2.2.0 GenomicAlignments_1.25.3 Rsamtools_2.5.3  GenomeInfoDbData_1.2.3 hms_0.5.3 grid_4.0.2  rpart_4.1-15 biovizBase_1.37.0 shiny_1.5.0  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:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  tximeta_1.7.14 tximport_1.17.6 SummarizedExperiment_1.19.6  DelayedArray_0.15.8 matrixStats_0.56.0 Matrix_1.2-18  Biobase_2.49.1 GenomicRanges_1.41.6 GenomeInfoDb_1.25.11  IRanges_2.23.10 S4Vectors_0.27.13 BiocGenerics_0.35.4 loaded via a namespace (and not attached):  httr_1.4.2 jsonlite_1.7.1 bit64_4.0.5  AnnotationHub_2.21.5 shiny_1.5.0 assertthat_0.2.1  askpass_1.1 interactiveDisplayBase_1.27.5 BiocManager_1.30.10  BiocFileCache_1.13.1 blob_1.2.1 Rsamtools_2.5.3  GenomeInfoDbData_1.2.3 yaml_2.2.1 progress_1.2.2  BiocVersion_3.12.0 pillar_1.4.6 RSQLite_2.2.0  lattice_0.20-41 glue_1.4.2 digest_0.6.25  promises_1.1.1 XVector_0.29.3 htmltools_0.5.0  httpuv_1.5.4 XML_3.99-0.5 pkgconfig_2.0.3  biomaRt_2.45.2 zlibbioc_1.35.0 purrr_0.3.4  xtable_1.8-4 later_188.8.131.52 BiocParallel_1.23.2  tibble_3.0.3 openssl_1.4.3 AnnotationFilter_1.13.0  generics_0.0.2 ellipsis_0.3.1 GenomicFeatures_1.41.3  lazyeval_0.2.2 magrittr_1.5 crayon_1.3.4  mime_0.9 memoise_1.1.0 evaluate_0.14  tools_4.0.2 prettyunits_1.1.1 hms_0.5.3  lifecycle_0.2.0 stringr_1.4.0 ensembldb_2.13.1  AnnotationDbi_1.51.3 Biostrings_2.57.2 compiler_4.0.2  tinytex_0.25 rlang_0.4.7 grid_4.0.2  RCurl_1.98-1.2 rstudioapi_0.11 rappdirs_0.3.1  bitops_1.0-6 rmarkdown_2.3 DBI_1.1.0  curl_4.3 R6_2.4.1 GenomicAlignments_1.25.3  rtracklayer_1.49.5 knitr_1.29 dplyr_1.0.2  fastmap_1.0.1 bit_4.0.4 ProtGenerics_1.21.0  stringi_1.5.3 Rcpp_1.0.5 vctrs_0.3.4  dbplyr_1.4.4 tidyselect_1.1.0 xfun_0.17
Suggestions are most welcome.