Hi,

I encountered an issue when using the catchSalmon() function from edgeR to import pseudo-alignment counts from the Salmon package. The counts were quantified using recent methods implemented in Salmon that allows the use of a decoy-aware transcriptome index. I currently have the latest versions of edgeR (3.26.7) and Salmon (0.14.1) installed.

The command I ran was:

salmon_counts <- catchSalmon(paths = dirs, verbose = TRUE)

For reference, the dirs object is a character vector of my Salmon quantification directories. However, it returned this error message:

Error in matrix(0, NTx, NSamples) : non-numeric matrix extent

I decided to first take a look and see where the error may have occurred in the source code. After calling body(catchSalmon) I found, to the best of my understanding, that catchSalmon() stores the meta_info.json file from the Salmon output directory into an object called Meta. It then records the number of transcripts using these commands which were implemented in a for loop (note: I only took the relevant lines of code for simplicity):

MetaFile <- file.path(paths[j], "aux_info", "meta_info.json")

Meta <- jsonlite::fromJSON(MetaFile)
NTx <- Meta$num_targets

But the meta_info.json file made by Salmon when using a decoy-aware index in the pseudo-alignment is slightly different. The previous term num_targets had been renamed to num_valid_targets (as there was a new term added in called num_decoy_targets as well).

I found that changing the line of code from catchSalmon():

NTx <- Meta$num_targets

to

NTx <- Meta$num_valid_targets

allowed the function to run without any issues.

I was hoping that this issue could possibly be addressed in a future update for edgeR, and so decided to make a post regarding it. I apologize in advance that this isn't exactly a proper question.

Thanks

R session info:

> 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_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] edgeR_3.26.7              swfdr_1.10.0              gridExtra_2.3             ggvis_0.4.4              
 [5] ggdendro_0.1-20           pheatmap_1.0.12           sva_3.32.1                BiocParallel_1.18.1      
 [9] genefilter_1.66.0         mgcv_1.8-28               nlme_3.1-141              DESeq_1.36.0             
[13] lattice_0.20-38           locfit_1.5-9.1            GSEABase_1.46.0           graph_1.62.0             
[17] annotate_1.62.0           XML_3.98-1.20             EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.8.0          
[21] AnnotationFilter_1.8.0    GenomicFeatures_1.36.4    AnnotationDbi_1.46.0      Biobase_2.44.0           
[25] GenomicRanges_1.36.0      GenomeInfoDb_1.20.0       IRanges_2.18.1            S4Vectors_0.22.0         
[29] here_0.1                  ggrepel_0.8.1             ggthemes_4.2.0            plotly_4.9.0             
[33] ggplot2_3.2.1             splitstackshape_1.4.8     RColorBrewer_1.1-2        biomaRt_2.40.3           
[37] tibble_2.1.3              readr_1.3.1               dplyr_0.8.3               magrittr_1.5             
[41] limma_3.40.6              AnnotationHub_2.16.0      BiocFileCache_1.8.0       dbplyr_1.4.2             
[45] BiocGenerics_0.30.0      

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1              rprojroot_1.3-2               XVector_0.24.0                rstudioapi_0.10              
 [5] bit64_0.9-7                   interactiveDisplayBase_1.22.0 fansi_0.4.0                   geneplotter_1.62.0           
 [9] knitr_1.24                    zeallot_0.1.0                 jsonlite_1.6                  Rsamtools_2.0.0              
[13] shiny_1.3.2                   BiocManager_1.30.4            compiler_3.6.1                httr_1.4.1                   
[17] backports_1.1.4               assertthat_0.2.1              Matrix_1.2-17                 lazyeval_0.2.2               
[21] cli_1.1.0                     later_0.8.0                   htmltools_0.3.6               prettyunits_1.0.2            
[25] tools_3.6.1                   gtable_0.3.0                  glue_1.3.1                    GenomeInfoDbData_1.2.1       
[29] reshape2_1.4.3                rappdirs_0.3.1                Rcpp_1.0.2                    vctrs_0.2.0                  
[33] Biostrings_2.52.0             rtracklayer_1.44.2            xfun_0.8                      stringr_1.4.0                
[37] mime_0.7                      zlibbioc_1.30.0               MASS_7.3-51.4                 scales_1.0.0                 
[41] hms_0.5.0                     promises_1.0.1                ProtGenerics_1.16.0           SummarizedExperiment_1.14.1  
[45] yaml_2.2.0                    curl_4.0                      memoise_1.1.0                 stringi_1.4.3                
[49] RSQLite_2.1.2                 rlang_0.4.0                   pkgconfig_2.0.2               matrixStats_0.54.0           
[53] bitops_1.0-6                  purrr_0.3.2                   labeling_0.3                  GenomicAlignments_1.20.1     
[57] htmlwidgets_1.3               bit_1.1-14                    tidyselect_0.2.5              plyr_1.8.4                   
[61] R6_2.4.0                      DelayedArray_0.10.0           DBI_1.0.0                     pillar_1.4.2                 
[65] withr_2.1.2                   survival_2.44-1.1             RCurl_1.95-4.12               crayon_1.3.4                 
[69] utf8_1.1.4                    progress_1.2.2                grid_3.6.1                    data.table_1.12.2            
[73] blob_1.2.0                    digest_0.6.20                 xtable_1.8-4                  tidyr_0.8.3                  
[77] httpuv_1.5.1                  munsell_0.5.0                 viridisLite_0.3.0