Entering edit mode
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
Hi Kevin, I've added the coldata output above in the original post
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).