Issue loading data with tximeta
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Entering edit mode
dshres • 0
@56442bb4
Last seen 16 hours ago
United States

I'm trying to load quants from salmon into RStudio using tximeta but I'm running into the error below.

>library(tximeta)

>indexDir <- file.path("rnaseq", "alt_quant", "sc_ensembl_index")
>fastaFTP <- c("ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz",
              "ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz")
>gtfPath <- file.path("rnaseq","tximeta_", "Mus_musculus.GRCm38.99.gtf.gz" )

>makeLinkedTxome(indexDir = indexDir,
                source   = "Ensembl", 
                organism = "Mus musculus", 
                release  = "99", 
                genome   = "GRCm38",
                fasta    = fastaFTP,
                gtf      = gtfPath,
                write    = FALSE)

>coldata <- read_csv("rnaseq_samples.csv")
>se <- tximeta(coldata)

importing quantifications
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 
found matching linked transcriptome:
[ Ensembl - Mus musculus - release 99 ]
loading existing EnsDb created: 2021-03-30 22:06:46
loading existing transcript ranges created: 2021-03-30 22:06:50
Error in validObject(.Object) : 
  invalid class "SummarizedExperiment" object: 
    'names(x)' must be NULL or have the length of 'x'

The rnaseq_samples.csv is a csv file with three columns labeled "names", "files", and "condition". I double-checked to make sure the filepaths weren't the problem. I also double-checked that the samples under "names" were characters and not numeric since a colleague pointed out that might be a problem.

>coldata
# A tibble: 12 x 3
   names files                                condition
   <chr> <chr>                                <chr>    
 1 511S  rnaseq/alt_quant/511S_quant/quant.sf C1       
 2 512S  rnaseq/alt_quant/512S_quant/quant.sf C2       
 3 525S  rnaseq/alt_quant/525S_quant/quant.sf C3       
 4 526S  rnaseq/alt_quant/526S_quant/quant.sf C4       
 5 535S  rnaseq/alt_quant/535S_quant/quant.sf C3       
 6 536S  rnaseq/alt_quant/536S_quant/quant.sf C4       
 7 546S  rnaseq/alt_quant/546S_quant/quant.sf C1       
 8 552S  rnaseq/alt_quant/552S_quant/quant.sf C2       
 9 574S  rnaseq/alt_quant/574S_quant/quant.sf C1       
10 575S  rnaseq/alt_quant/575S_quant/quant.sf C2       
11 586S  rnaseq/alt_quant/586S_quant/quant.sf C4       
12 587S  rnaseq/alt_quant/587S_quant/quant.sf C3 

>all(file.exists(coldata$files))
[1] TRUE

This is my sessionInfo() output, any help to fix the error above would be appreciated!

>sessionInfo( )

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] kableExtra_1.3.1           
 [2] pheatmap_1.0.12            
 [3] readr_1.4.0                
 [4] ggplot2_3.3.3              
 [5] dplyr_1.0.2                
 [6] DESeq2_1.28.1              
 [7] tximeta_1.6.3              
 [8] SummarizedExperiment_1.18.2
 [9] DelayedArray_0.14.1        
[10] matrixStats_0.57.0         
[11] Biobase_2.50.0             
[12] GenomicRanges_1.40.0       
[13] GenomeInfoDb_1.24.2        
[14] IRanges_2.24.0             
[15] S4Vectors_0.28.1           
[16] BiocGenerics_0.36.0        

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.20.0          
 [2] bitops_1.0-6                 
 [3] bit64_4.0.5                  
 [4] webshot_0.5.2                
 [5] RColorBrewer_1.1-2           
 [6] progress_1.2.2               
 [7] httr_1.4.2                   
 [8] tools_4.0.2                  
 [9] R6_2.5.0                     
[10] colorspace_2.0-0             
[11] DBI_1.1.0                    
[12] lazyeval_0.2.2               
[13] withr_2.3.0                  
[14] tidyselect_1.1.0             
[15] prettyunits_1.1.1            
[16] bit_4.0.4                    
[17] curl_4.3                     
[18] compiler_4.0.2               
[19] rvest_0.3.6                  
[20] xml2_1.3.2                   
[21] rtracklayer_1.48.0           
[22] scales_1.1.1                 
[23] genefilter_1.70.0            
[24] askpass_1.1                  
[25] rappdirs_0.3.1               
[26] stringr_1.4.0                
[27] digest_0.6.27                
[28] Rsamtools_2.4.0              
[29] rmarkdown_2.5                
[30] XVector_0.30.0               
[31] pkgconfig_2.0.3              
[32] htmltools_0.5.0              
[33] dbplyr_1.4.4                 
[34] fastmap_1.0.1                
[35] ensembldb_2.12.1             
[36] rlang_0.4.9                  
[37] rstudioapi_0.13              
[38] RSQLite_2.2.1                
[39] shiny_1.5.0                  
[40] generics_0.1.0               
[41] jsonlite_1.7.2               
[42] BiocParallel_1.22.0          
[43] RCurl_1.98-1.2               
[44] magrittr_2.0.1               
[45] GenomeInfoDbData_1.2.3       
[46] Matrix_1.2-18                
[47] munsell_0.5.0                
[48] Rcpp_1.0.5                   
[49] lifecycle_0.2.0              
[50] stringi_1.5.3                
[51] yaml_2.2.1                   
[52] zlibbioc_1.36.0              
[53] BiocFileCache_1.12.1         
[54] AnnotationHub_2.20.2         
[55] grid_4.0.2                   
[56] blob_1.2.1                   
[57] promises_1.1.1               
[58] crayon_1.3.4                 
[59] lattice_0.20-41              
[60] Biostrings_2.58.0            
[61] splines_4.0.2                
[62] GenomicFeatures_1.40.1       
[63] annotate_1.66.0              
[64] hms_0.5.3                    
[65] locfit_1.5-9.4               
[66] knitr_1.30                   
[67] pillar_1.4.7                 
[68] geneplotter_1.66.0           
[69] biomaRt_2.44.4               
[70] XML_3.99-0.5                 
[71] glue_1.4.2                   
[72] BiocVersion_3.11.1           
[73] evaluate_0.14                
[74] BiocManager_1.30.10          
[75] vctrs_0.3.5                  
[76] httpuv_1.5.4                 
[77] gtable_0.3.0                 
[78] openssl_1.4.3                
[79] purrr_0.3.4                  
[80] assertthat_0.2.1             
[81] xfun_0.19                    
[82] mime_0.9                     
[83] xtable_1.8-4                 
[84] AnnotationFilter_1.12.0      
[85] later_1.1.0.1                
[86] viridisLite_0.3.0            
[87] survival_3.1-12              
[88] tibble_3.0.4                 
[89] GenomicAlignments_1.24.0     
[90] AnnotationDbi_1.50.3         
[91] memoise_1.1.0                
[92] tximport_1.16.1              
[93] ellipsis_0.3.1               
[94] interactiveDisplayBase_1.26.3
tximeta • 87 views
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@kevin
Last seen 28 minutes ago
Ireland, Republic of

Hi, can you please show the output of coldata?

Kevin

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Entering edit mode

Hi Kevin, I've added the coldata output above in the original post

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Entering edit mode

Thanks. Are you able to get a minimal example working, if even by following the vignette? - https://bioconductor.org/packages/devel/bioc/vignettes/tximeta/inst/doc/tximeta.html

You also seem to have many packages loaded. It's a good idea to restart your R session for every new analysis (apologies if this comment is not relevant to your situation).

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