chunxubioinfor
commented
10 months ago Hi Erick, I noticed your vroom version is 1.6.4. Could you downgrade the vroom to 1.6.3. ? This error should be solved by that. Btw which version of IsoformSwitchAnalyzeR did you use? We updated the tool recently, and you can easily download and update it from github :)
ErickMUO
Hi,
Thank you for developing a tool that addresses the exploration of Isoform usage analysis. I want to give it a try to the tool, and at the beginning, I started with my own data using Kallisto pseudoalignment for several datasets. However, I encountered the following error:
Import all quantifications stored in a folder
Step 1 of 3: Identifying which algorithm was used... The quantification algorithm used was: Kallisto Found 24 quantification file(s) of interest Step 2 of 3: Reading data... Note: importing
abundance.h5is typically faster thanabundance.tsvreading in files with read_tsv1 Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, :
bad value
Step 1 of 3: Identifying which algorithm was used... The quantification algorithm used was: Kallisto Found 32 quantification file(s) of interest Step 2 of 3: Reading data... Note: importing
abundance.h5is typically faster thanabundance.tsvreading in files with read_tsv1 Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, :
bad value
Initially, I suspected that the issue was related to my own data, so I proceeded to try with the data allocated in the package. Surprisingly, I encountered the same error with the package data as well.
I tried to look for a solution in the tximport package since I understand it is a wrapper for the tximport package, and I came across this solution: https://support.bioconductor.org/p/9154550/#9154571
I attempted to use the parameter mentioned there (importer = read.delim), but it appears that this parameter is not supported for the importIsoformExpression() function.
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Stockholm tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] IsoformSwitchAnalyzeR_2.0.1 pfamAnalyzeR_1.0.1 dplyr_1.1.3
[4] stringr_1.5.0 readr_2.1.4 ggplot2_3.4.3
[7] sva_3.48.0 genefilter_1.82.1 mgcv_1.9-0
[10] nlme_3.1-163 satuRn_1.8.0 DEXSeq_1.46.0
[13] RColorBrewer_1.1-3 AnnotationDbi_1.62.2 DESeq2_1.40.2
[16] SummarizedExperiment_1.30.2 GenomicRanges_1.52.0 GenomeInfoDb_1.36.3
[19] IRanges_2.34.1 S4Vectors_0.38.2 MatrixGenerics_1.12.3
[22] matrixStats_1.0.0 Biobase_2.60.0 BiocGenerics_0.46.0
[25] BiocParallel_1.34.2 limma_3.56.2
loaded via a namespace (and not attached): [1] vroom_1.6.4 progress_1.2.2
[3] pacman_0.5.1 vsn_3.68.0
[5] locfdr_1.1-8 goftest_1.2-3
[7] Biostrings_2.68.1 vctrs_0.6.3
[9] spatstat.random_3.1-6 digest_0.6.33
[11] png_0.1-8 ggrepel_0.9.3
[13] deldir_1.0-9 parallelly_1.36.0
[15] MASS_7.3-60 reshape2_1.4.4
[17] httpuv_1.6.11 qvalue_2.32.0
[19] withr_2.5.1 ggfun_0.1.3
[21] ellipsis_0.3.2 survival_3.5-7
[23] memoise_2.0.1 tximeta_1.18.3
[25] clusterProfiler_4.8.2 gson_0.1.0
[27] tidytree_0.4.5 zoo_1.8-12
[29] pbapply_1.7-2 prettyunits_1.2.0
[31] KEGGREST_1.40.1 promises_1.2.1
[33] httr_1.4.7 downloader_0.4
[35] restfulr_0.0.15 globals_0.16.2
[37] fitdistrplus_1.1-11 rhdf5filters_1.12.1
[39] rhdf5_2.44.0 rstudioapi_0.15.0
[41] miniUI_0.1.1.1 generics_0.1.3
[43] DOSE_3.26.1 reactome.db_1.84.0
[45] curl_5.1.0 zlibbioc_1.46.0
[47] ggraph_2.1.0 polyclip_1.10-6
[49] GenomeInfoDbData_1.2.10 ExperimentHub_2.8.1
[51] interactiveDisplayBase_1.38.0 xtable_1.8-4
[53] S4Arrays_1.0.6 BiocFileCache_2.8.0
[55] preprocessCore_1.62.1 hms_1.1.3
[57] irlba_2.3.5.1 colorspace_2.1-0
[59] filelock_1.0.2 ROCR_1.0-11
[61] VennDiagram_1.7.3 reticulate_1.32.0
[63] spatstat.data_3.0-1 magrittr_2.0.3
[65] lmtest_0.9-40 later_1.3.1
[67] viridis_0.6.4 ggtree_3.8.2
[69] lattice_0.21-9 spatstat.geom_3.2-5
[71] future.apply_1.11.0 scattermore_1.2
[73] XML_3.99-0.14 shadowtext_0.1.2
[75] cowplot_1.1.1 RcppAnnoy_0.0.21
[77] pillar_1.9.0 compiler_4.3.0
[79] stringi_1.7.12 tensor_1.5
[81] GenomicAlignments_1.36.0 plyr_1.8.9
[83] crayon_1.5.2 abind_1.4-5
[85] BiocIO_1.10.0 gridGraphics_0.5-1
[87] locfit_1.5-9.8 sp_2.1-0
[89] graphlayouts_1.0.1 bit_4.0.5
[91] fastmatch_1.1-4 codetools_0.2-19
[93] plotly_4.10.2 mime_0.12
[95] splines_4.3.0 Rcpp_1.0.11
[97] dbplyr_2.3.4 sparseMatrixStats_1.12.2
[99] HDO.db_0.99.1 blob_1.2.4
[101] utf8_1.2.3 BiocVersion_3.17.1
[103] AnnotationFilter_1.24.0 fs_1.6.3
[105] listenv_0.9.0 DelayedMatrixStats_1.22.6
[107] ggplotify_0.1.2 tibble_3.2.1
[109] Matrix_1.6-1.1 statmod_1.5.0
[111] tzdb_0.4.0 tweenr_2.0.2
[113] pkgconfig_2.0.3 pheatmap_1.0.12
[115] tools_4.3.0 cachem_1.0.8
[117] RSQLite_2.3.1 viridisLite_0.4.2
[119] DBI_1.1.3 celldex_1.10.1
[121] graphite_1.46.0 fastmap_1.1.1
[123] scales_1.2.1 grid_4.3.0
[125] ica_1.0-3 geneplotter_1.78.0
[127] Seurat_4.4.0 Rsamtools_2.16.0
[129] AnnotationHub_3.8.0 patchwork_1.1.3
[131] BiocManager_1.30.22 graph_1.78.0
[133] RANN_2.6.1 farver_2.1.1
[135] tidygraph_1.2.3 scatterpie_0.2.1
[137] yaml_2.3.7 rtracklayer_1.60.1
[139] cli_3.6.1 purrr_1.0.2
[141] leiden_0.4.3 lifecycle_1.0.3
[143] uwot_0.1.16 lambda.r_1.2.4
[145] tximport_1.28.0 annotate_1.78.0
[147] MeSHDbi_1.36.0 gtable_0.3.4
[149] rjson_0.2.21 ggridges_0.5.4
[151] progressr_0.14.0 parallel_4.3.0
[153] ape_5.7-1 jsonlite_1.8.7
[155] edgeR_3.42.4 bitops_1.0-7
[157] progeny_1.22.0 bit64_4.0.5
[159] depmap_1.14.0 Rtsne_0.16
[161] yulab.utils_0.1.0 ReactomePA_1.44.0
[163] spatstat.utils_3.0-3 SeuratObject_4.1.4
[165] futile.options_1.0.1 GOSemSim_2.26.1
[167] lazyeval_0.2.2 shiny_1.7.5
[169] htmltools_0.5.6.1 affy_1.78.2
[171] enrichplot_1.20.0 GO.db_3.17.0
[173] sctransform_0.4.0 rappdirs_0.3.3
[175] formatR_1.14 ensembldb_2.24.1
[177] glue_1.6.2 XVector_0.40.0
[179] RCurl_1.98-1.12 treeio_1.24.3
[181] BSgenome_1.68.0 futile.logger_1.4.3
[183] gridExtra_2.3 boot_1.3-28.1
[185] igraph_1.5.1 R6_2.5.1
[187] tidyr_1.3.0 GenomicFeatures_1.52.2
[189] cluster_2.1.4 Rhdf5lib_1.22.1
[191] aplot_0.2.2 DelayedArray_0.26.7
[193] tidyselect_1.2.0 ProtGenerics_1.32.0
[195] ggforce_0.4.1 xml2_1.3.5
[197] future_1.33.0 munsell_0.5.0
[199] KernSmooth_2.23-22 affyio_1.70.0
[201] data.table_1.14.8 htmlwidgets_1.6.2
[203] fgsea_1.26.0 hwriter_1.3.2.1
[205] biomaRt_2.56.1 rlang_1.1.1
[207] spatstat.sparse_3.0-2 spatstat.explore_3.2-3
[209] fansi_1.0.5