DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
0
2
Entering edit mode
Dakarai ▴ 10
@05ba1bde
Last seen 2.0 years ago
United States

I am trying to perform differential exon usage analysis using DEXSeq. I cannot create a DEXSeqDataset object using count files generated from dexseq_count.py and gff file generated from dexseq_prepare_annotation.py. I found other questions where the suggestion was to check if there was a discrepancy betweem the number of lines in count files and lines corresponding to 'exonic_part' in the gff file. I've checked this and found that all counts files match and correspond with the gff file. Can anyone offer a suggestion to fix this?

My code returns: Error in FUN(X[[i]], ...) : subscript out of bounds

#Output of list.files() in working directory
 "3-31-22input_juncs_DI_pA_all_exons.filtered.gff"                                                                                                                  "KO_1_8.counts.txt"   "KO_3_1.counts.txt" "KO_3_2.counts.txt"                                                                                                      "KO_3_3.counts.txt" "WT_3_6.counts.txt"                                                                                                                                              "WT_3_7.counts.txt"   "WT_3_8.counts.txt"   

countFiles <- list.files(pattern = '.counts', full.names=TRUE)
flattenedFile <- list.files(pattern-'.gff',full.names=TRUE)

sampleTable <- data.frame(row.names=c('KO_1_8','KO_3_1','KO_3_2','KO_3_3','WT_1_7','WT_3_6','WT_3_7','WT_3_8'), condition = c('KO','KO','KO','KO','WT','WT','WT','WT'),libType = c('paired-end','paired-end','paired-end','paired-end','paired-end','paired-end','paired-end','paired-end'))

dxd <- DEXSeqDataSetFromHTSeq(countFiles, 
sampleData=sampleTable, design= ~sample+exon+condition:exon, flattenedfile=flattenedFile) #problematic line

#output of sessionInfo( ):

R version 4.1.3 (2022-03-10)                                                                                                                                            Platform: x86_64-pc-linux-gnu (64-bit)                                                                                                                                  Running under: Ubuntu 20.04.3 LTS                                                                                                                                                                                                                                                                                                               Matrix products: default                                                                                                                                                BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0                                                                                                                 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0                                                                                                                                                                                                                                                                                     locale:                                                                                                                                                                  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8                                                                                                       [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8                                                                                                   [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C                                                                                                         [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C                                                                                                                                                                                                                                                                          attached base packages:                                                                                                                                                 [1] stats4    stats     graphics  grDevices utils     datasets  methods                                                                                                 [8] base                                                                                                                                                                                                                                                                                                                                        other attached packages:                                                                                                                                                 [1] DEXSeq_1.40.0               RColorBrewer_1.1-3                                                                                                                      [3] AnnotationDbi_1.56.2        DESeq2_1.34.0                                                                                                                           [5] SummarizedExperiment_1.24.0 GenomicRanges_1.46.1                                                                                                                    [7] GenomeInfoDb_1.30.1         IRanges_2.28.0                                                                                                                          [9] S4Vectors_0.32.4            MatrixGenerics_1.6.0                                                                                                                   [11] matrixStats_0.61.0          Biobase_2.54.0                                                                                                                         [13] BiocGenerics_0.40.0         BiocParallel_1.28.3                                                                                                                                                                                                                                                                                            loaded via a namespace (and not attached):                                                                                                                               [1] httr_1.4.2             bit64_4.0.5            splines_4.1.3                                                                                                         [4] assertthat_0.2.1       statmod_1.4.36         BiocFileCache_2.2.1                                                                                                   [7] blob_1.2.2             Rsamtools_2.10.0       GenomeInfoDbData_1.2.7                                                                                               [10] progress_1.2.2         pillar_1.7.0           RSQLite_2.2.12                                                                                                       [13] lattice_0.20-45        glue_1.6.2             digest_0.6.29                                                                                                        [16] XVector_0.34.0         colorspace_2.0-3       Matrix_1.4-1                                                                                                         [19] XML_3.99-0.9           pkgconfig_2.0.3        biomaRt_2.50.3                                                                                                       [22] genefilter_1.76.0      zlibbioc_1.40.0        purrr_0.3.4                                                                                                          [25] xtable_1.8-4           scales_1.1.1           tibble_3.1.6                                                                                                         [28] annotate_1.72.0        KEGGREST_1.34.0        generics_0.1.2                                                                                                       [31] ggplot2_3.3.5          ellipsis_0.3.2         cachem_1.0.6                                                                                                         [34] cli_3.2.0              survival_3.3-1         magrittr_2.0.3                                                                                                       [37] crayon_1.5.1           memoise_2.0.1          fansi_1.0.3                                                                                                          [40] xml2_1.3.3             hwriter_1.3.2          tools_4.1.3                                                                                                          [43] prettyunits_1.1.1      hms_1.1.1              lifecycle_1.0.1                                                                                                      [46] stringr_1.4.0          munsell_0.5.0          locfit_1.5-9.5                                                                                                       [49] DelayedArray_0.20.0    Biostrings_2.62.0      compiler_4.1.3                                                                                                       [52] rlang_1.0.2            grid_4.1.3             RCurl_1.98-1.6                                                                                                       [55] rappdirs_0.3.3         bitops_1.0-7           gtable_0.3.0                                                                                                         [58] curl_4.3.2             DBI_1.1.2              R6_2.5.1                                                                                                             [61] dplyr_1.0.8            fastmap_1.1.0          bit_4.0.4                                                                                                            [64] utf8_1.2.2             filelock_1.0.2         stringi_1.7.6                                                                                                        [67] parallel_4.1.3         Rcpp_1.0.8.3           vctrs_0.4.0                                                                                                          [70] geneplotter_1.72.0     png_0.1-7              dbplyr_2.1.1                                                                                                         [73] tidyselect_1.1.2
R DEXSeq SequenceAnnotation RNASeqData • 973 views
ADD COMMENT
1
Entering edit mode

Hello! I had the same issue it was answered. Its the quotes made by newer versions of HTSeq. See Arthur's answer here: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq) Good luck!!

ADD REPLY
0
Entering edit mode

Thank you so much! Sorry for the late response, was pulled away by some other work.

ADD REPLY

Login before adding your answer.

Traffic: 780 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6