RStudio, R and all packages downloaded and installed this week
Following along with DIYtranscriptomics https://diytranscriptomics.com/scripts (lesson 1) which is superb (highly recommended), but I'm having issues. I know the key part of the error is
"attempt to set 'colnames' on an object with less than two dimensions" but I don't know what that's referring to or what I can do to fix it. I have run this programme previously with success (~9 months ago) but I'm trying with my own samples now, and it's not working.
# copy the abundance files to the working directory and rename so that each sample has a unique name > Txi_gene.D.labrax <- tximport(path.D.labrax.all, + type = "kallisto", + tx2gene = "Tx", + txOut = FALSE, + countsFromAbundance = "lengthScaledTPM", + ignoreTxVersion = TRUE) Note: importing `abundance.h5` is typically faster than `abundance.tsv` reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 Error in `colnames<-`(`*tmp*`, value = c("tx", "gene")) : attempt to set 'colnames' on an object with less than two dimensions
I have checked the file paths:
> all(file.exists(path.D.labrax.all))  TRUE
And that all seems fine, and everything up until this point has worked. Googling the error hasn't helped though. Having looked at ?colnames the issue seems to be what is the
*tmp* variable is and where it comes from. The tximport reads in the files OK I think (12 files, and it counts them in, so I'm guessing that's OK)
colnames(x, do.NULL=TRUE, prefix="col") colnames(x) <- value
x A matrix-like object.
do.NULL, prefix See ?base::rownames for a description of these arguments. value Either NULL or a character vector equal of length equal to the appropriate dimension.
Session info included below.
> 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:  LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C  LC_TIME=English_Australia.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  tximport_1.18.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4 readr_1.4.0 tibble_3.1.2  ggplot2_3.3.3 tidyverse_1.3.1 tidyr_1.1.3 biomaRt_2.46.3 clusterProfiler_3.18.1 cowplot_1.1.1 beepr_1.3  BiocManager_1.30.15 Biobase_2.50.0 BiocGenerics_0.36.1 magrittr_2.0.1 loaded via a namespace (and not attached):  fgsea_1.16.0 colorspace_2.0-1 ellipsis_0.3.2 qvalue_2.22.0 fs_1.5.0 rstudioapi_0.13 farver_2.1.0  audio_0.1-7 graphlayouts_0.7.1 ggrepel_0.9.1 bit64_4.0.5 AnnotationDbi_1.52.0 fansi_0.5.0 scatterpie_0.1.6  lubridate_1.7.10 xml2_1.3.2 splines_4.0.4 cachem_1.0.5 GOSemSim_2.16.1 knitr_1.33 polyclip_1.10-0  jsonlite_1.7.2 broom_0.7.6 GO.db_3.12.1 dbplyr_2.1.1 ggforce_0.3.3 compiler_4.0.4 httr_1.4.2  rvcheck_0.1.8 backports_1.2.1 assertthat_0.2.1 Matrix_1.3-3 fastmap_1.1.0 cli_2.5.0 tweenr_1.0.2  htmltools_0.5.1.1 prettyunits_1.1.1 tools_4.0.4 igraph_1.2.6 gtable_0.3.0 glue_1.4.2 reshape2_1.4.4  DO.db_2.9 rappdirs_0.3.3 tinytex_0.32 fastmatch_1.1-0 Rcpp_1.0.6 enrichplot_1.10.2 cellranger_1.1.0  rhdf5filters_1.2.1 vctrs_0.3.8 ggraph_2.0.5 xfun_0.23 rvest_1.0.0 lifecycle_1.0.0 XML_3.99-0.6  DOSE_3.16.0 MASS_7.3-54 scales_1.1.1 tidygraph_1.2.0 hms_1.1.0 rhdf5_2.34.0 RColorBrewer_1.1-2  yaml_2.2.1 curl_4.3.1 memoise_2.0.0 gridExtra_2.3 downloader_0.4 stringi_1.5.3 RSQLite_2.2.7  S4Vectors_0.28.1 BiocParallel_1.24.1 rlang_0.4.11 pkgconfig_2.0.3 evaluate_0.14 lattice_0.20-44 Rhdf5lib_1.12.1  shadowtext_0.0.8 bit_4.0.4 tidyselect_1.1.1 plyr_1.8.6 R6_2.5.0 IRanges_2.24.1 generics_0.1.0  DBI_1.1.1 pillar_1.6.1 haven_2.4.1 withr_2.4.2 modelr_0.1.8 crayon_1.4.1 utf8_1.2.1  BiocFileCache_1.14.0 rmarkdown_2.8 viridis_0.6.1 progress_1.2.2 grid_4.0.4 readxl_1.3.1 data.table_1.14.0  blob_1.2.1 reprex_2.0.0 digest_0.6.27 openssl_1.4.4 stats4_4.0.4 munsell_0.5.0 viridisLite_0.4.0  askpass_1.1