我正在跟随 DIYTranscriptomics
我无法让 Tximport 在我自己的样本上运行。我运行下面的代码，并得到以下输出。
> Txi_gene.D.labrax <- tximport(path.D.labrax.3,
+ type = "kallisto",
+ tx2gene = Tx.D.labrax,
+ txOut = FALSE,
+ countsFromAbundance = "lengthScaledTPM",
+ ignoreTxVersion = TRUE,
+ ignoreAfterBar = TRUE)
Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read_tsv
1 2 3
Error in .local(object, ...) :
None of the transcripts in the quantification files are present
in the first column of tx2gene. Check to see that you are using
the same annotation for both.
Example IDs (file): [ENSDLAT00005064321, ENSDLAT00005064323, ENSDLAT00005005748, ...]
Example IDs (tx2gene): [ENSDLAT00005000002.1, ENSDLAT00005000003.1, ENSDLAT00005000004.1, ...]
This can sometimes (not always) be fixed using 'ignoreTxVersion' or 'ignoreAfterBar'.
我不明白的是，当我在 tsv 文件中手动搜索从 Ensembl 转录组创建的 tibble 中的转录时，例如 ENSDLAT005example，我可以找到它，反之亦然。在 tsv 和 tibble 中，这两列都称为 target_id。我不知道从这里去哪里。它应该工作，但事实并非如此。所有这些东西都在过去两周内完成/安装，所以我确信我没有使用过时的包或其他东西。
sessionInfo( )
> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tximport_1.18.0 biomaRt_2.46.3
loaded via a namespace (and not attached):
[1] progress_1.2.2 tinytex_0.32 tidyselect_1.1.1 xfun_0.23 purrr_0.3.4
[6] rhdf5_2.34.0 vctrs_0.3.8 generics_0.1.0 htmltools_0.5.1.1 stats4_4.0.4
[11] BiocFileCache_1.14.0 yaml_2.2.1 utf8_1.2.1 blob_1.2.1 XML_3.99-0.6
[16] rlang_0.4.11 pillar_1.6.1 glue_1.4.2 DBI_1.1.1 rappdirs_0.3.3
[21] BiocGenerics_0.36.1 bit64_4.0.5 dbplyr_2.1.1 lifecycle_1.0.0 stringr_1.4.0
[26] memoise_2.0.0 evaluate_0.14 Biobase_2.50.0 knitr_1.33 IRanges_2.24.1
[31] fastmap_1.1.0 parallel_4.0.4 curl_4.3.1 AnnotationDbi_1.52.0 fansi_0.5.0
[36] Rcpp_1.0.6 readr_1.4.0 openssl_1.4.4 cachem_1.0.5 S4Vectors_0.28.1
[41] bit_4.0.4 hms_1.1.0 askpass_1.1 digest_0.6.27 stringi_1.5.3
[46] dplyr_1.0.6 rhdf5filters_1.2.1 tools_4.0.4 magrittr_2.0.1 RSQLite_2.2.7
[51] tibble_3.1.2 crayon_1.4.1 pkgconfig_2.0.3 ellipsis_0.3.2 xml2_1.3.2
[56] prettyunits_1.1.1 assertthat_0.2.1 rmarkdown_2.8 httr_1.4.2 Rhdf5lib_1.12.1
[61] R6_2.5.0 compiler_4.0.4