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Hi folks,
I am having some issues using tximport to make a counts object from salmon outputs to feed into DESEQ2. When I try to use the tximport function on a list of files corresponding to salmon outputs the resulting occurs:
> txi <- tximport(files[1], type="salmon", tx2gene=tx2gene) reading in files with read_tsv 1 Error: package_version(minfo$salmon_version) >= "0.8.0" is not TRUE > txi Error: object 'txi' not found
I did, in fact, use a salmon version <= 0.8.0 (0.7.2 to be precise) as it was the most recent version available on my institution's HPC. Is there a work around or alternative package/ function to use for the lower version? Or does some additional functionality exist in salmon version 0.8.0 and higher that is required and thus I should just get that version installed and re run salmon.
Thanks in advance for any help and suggestions,
Adam Getzler
Graduate Student
Hi Michael,
Setting dropInfReps=TRUE solved the problem.
Thanks!
Adam
Dear Michael I have the same problem,as you mentioned i tried the dropInfReps=TRUE but that is not solved yet. The session info: R version 3.5.2 (2018-12-20) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 7 (build 7600)
Matrix products: default
locale: [1] LCCOLLATE=EnglishUnited States.1252 [2] LCCTYPE=EnglishUnited States.1252
[3] LCMONETARY=EnglishUnited States.1252 [4] LCNUMERIC=C
[5] LCTIME=English_United States.1252
attached base packages: [1] parallel stats4 stats
[4] graphics grDevices utils
[7] datasets methods base
other attached packages: [1] DESeq21.22.2
[2] SummarizedExperiment1.12.0 [3] DelayedArray0.8.0
[4] BiocParallel1.16.6
[5] matrixStats0.54.0
[6] Biobase2.42.0
[7] GenomicRanges1.34.0
[8] GenomeInfoDb1.18.2
[9] IRanges2.16.0
[10] S4Vectors0.20.1
[11] BiocGenerics0.28.0
[12] tximportData1.10.0
[13] readr1.3.1
[14] tximport1.10.1
loaded via a namespace (and not attached): [1] Rcpp1.0.0
[2] Formula1.2-3
[3] knitr1.22
[4] XVector0.22.0
[5] magrittr1.5
[6] cluster2.0.7-1
[7] GenomicAlignments1.18.1 [8] splines3.5.2
[9] progress1.2.0
[10] hms0.4.2
[11] zlibbioc1.28.0
[12] tidyselect0.2.5
[13] bit1.1-14
[14] xtable1.8-3
[15] colorspace1.4-0
[16] biovizBase1.30.1
[17] lattice0.20-38
[18] BSgenome1.50.0
[19] R62.4.0
[20] rlang0.3.1
[21] xfun0.5
[22] latticeExtra0.6-28
[23] genefilter1.64.0
[24] ProtGenerics1.14.0
[25] htmltools0.3.6
[26] assertthat0.2.0
[27] bit640.9-7
[28] digest0.6.18
[29] tibble2.0.1
[30] Matrix1.2-16
[31] Gviz1.26.5
[32] acepack1.4.1
[33] curl3.3
[34] RCurl1.95-4.12
[35] compiler3.5.2
[36] pillar1.3.1
[37] backports1.1.3
[38] scales1.0.0
[39] prettyunits1.0.2
[40] Hmisc4.2-0
[41] Biostrings2.50.2
[42] Rsamtools1.34.1
[43] GenomicFeatures1.34.4
[44] locfit1.5-9.1
[45] annotate1.60.1
[46] jsonlite1.6
[47] pkgconfig2.0.2
[48] AnnotationDbi1.44.0
[49] rstudioapi0.9.0
[50] munsell0.5.0
[51] ensembldb2.6.7
[52] blob1.1.1
[53] httr1.4.0
[54] plyr1.8.4
[55] dplyr0.8.0.1
[56] stringr1.4.0
[57] tools3.5.2
[58] dichromat2.0-0
[59] nnet7.3-12
[60] grid3.5.2
[61] cummeRbund2.24.0
[62] data.table1.12.0
[63] checkmate1.9.1
[64] htmlTable1.13.1
[65] gtable0.2.0
[66] DBI1.0.0
[67] lazyeval0.2.1
[68] survival2.43-3
[69] crayon1.3.4
[70] gridExtra2.3
[71] GenomeInfoDbData1.2.0
[72] geneplotter1.60.0
[73] AnnotationFilter1.6.0
[74] purrr0.3.1
[75] ggplot23.1.0
[76] rtracklayer1.42.2
[77] RColorBrewer1.1-2
[78] htmlwidgets1.3
[79] bitops1.0-6
[80] base64enc0.1-3
[81] rpart4.1-13
[82] biomaRt2.38.0
[83] glue1.3.1
[84] RSQLite2.1.1
[85] memoise1.1.0
[86] stringi1.4.3
[87] XML3.98-1.19
[88] VariantAnnotation1.28.11 [89] foreign_0.8-71
What shall i do now? Thanks a lot in advance, Elmira
I would strongly recommend to use a more recent version of Salmon. This is going back to a version that predates the current import functions. Versions < 0.8.0 are more than 2 years old, and there have been many bug fixes and improvements in the software since this version of Salmon. I will say thought that it's possible to import any kind of data using the manual column specifications and
type="none"(see ?tximport).Dear Michael Thank you so much for your kind reply. You are right,that was old version,i will try latest version of salmon.Also,I run the following command,it worked. txi <- tximport(files, type = "none", txOut = TRUE, txIdCol = "Name", abundanceCol = "TPM", countsCol = "NumReads", lengthCol = "Length", tx2gene = tx2gene,importer = read_tsv) Kind Regards, Elmira