DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
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Delta._.43 ▴ 20
@a6fd600c
Last seen 5 weeks ago
Poland

Reading in data generated with dexseq_count.py using DEXSeqDataSetFromHTSeq() throws the following error:

Error in FUN(X[[i]], ...) : subscript out of bounds
 4. lapply(X = X, FUN = FUN, ...)
 3. sapply(splitted, "[[", 2)
 2. sapply(splitted, "[[", 2)
 1. DEXSeqDataSetFromHTSeq(countFiles, sampleData = sampleTable, 
    design = ~sample + exon + condition:exon, flattenedfile = flattenedFile)

Based on the traceback it leads back to the line where it reads the count files inside the function -

lf <- lapply(countfiles, function(x) read.table(x, header = FALSE, 
        stringsAsFactors = FALSE))

For some reason the default behaviour of read.table() splits the file into 3 columns rather than 2 as originally intended. Specifying the delimiter for the file explicitly solves the issue. i.e.

lf <- lapply(countfiles, function(x) read.table(x, header = FALSE, 
        stringsAsFactors = FALSE, sep = '\t'))

I'm not sure where to post this fix or if this is the best way to solve this issue. Maybe someone with more experience could provide a better solution.


dxd = DEXSeqDataSetFromHTSeq(
   countFiles,
   sampleData=sampleTable,
   design= ~ sample + exon + condition:exon,
   flattenedfile=flattenedFile )

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

traceback()

$ 4: lapply(X = X, FUN = FUN, ...)
$ 3: sapply(splitted, "[[", 2)
$ 2: sapply(splitted, "[[", 2)
$ 1: DEXSeqDataSetFromHTSeq(countFiles, sampleData = sampleTable, 
       design = ~sample + exon + condition:exon, flattenedfile = flattenedFile)


sessionInfo()

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.utf8  LC_CTYPE=English_India.utf8    LC_MONETARY=English_India.utf8 LC_NUMERIC=C                   LC_TIME=English_India.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.42.0               RColorBrewer_1.1-3          AnnotationDbi_1.58.0        DESeq2_1.36.0               SummarizedExperiment_1.26.1
 [6] GenomicRanges_1.48.0        GenomeInfoDb_1.32.2         IRanges_2.30.0              S4Vectors_0.34.0            MatrixGenerics_1.8.1       
[11] matrixStats_0.62.0          Biobase_2.56.0              BiocGenerics_0.42.0         BiocParallel_1.30.3         reshape2_1.4.4             
[16] kableExtra_1.3.4            forcats_0.5.1               stringr_1.4.0               dplyr_1.0.9                 purrr_0.3.4                
[21] readr_2.1.2                 tidyr_1.2.0                 tibble_3.1.8                ggplot2_3.3.6               tidyverse_1.3.2            
[26] data.table_1.14.2          

loaded via a namespace (and not attached):
 [1] googledrive_2.0.0      colorspace_2.0-3       hwriter_1.3.2.1        ellipsis_0.3.2         XVector_0.36.0         fs_1.5.2              
 [7] rstudioapi_0.13        bit64_4.0.5            fansi_1.0.3            lubridate_1.8.0        xml2_1.3.3             codetools_0.2-18      
[13] splines_4.2.1          cachem_1.0.6           geneplotter_1.74.0     knitr_1.39             jsonlite_1.8.0         Rsamtools_2.12.0      
[19] broom_1.0.0            annotate_1.74.0        dbplyr_2.2.1           png_0.1-7              compiler_4.2.1         httr_1.4.3            
[25] backports_1.4.1        assertthat_0.2.1       Matrix_1.4-1           fastmap_1.1.0          gargle_1.2.0           cli_3.3.0             
[31] prettyunits_1.1.1      htmltools_0.5.3        tools_4.2.1            gtable_0.3.0           glue_1.6.2             GenomeInfoDbData_1.2.8
[37] rappdirs_0.3.3         Rcpp_1.0.9             cellranger_1.1.0       vctrs_0.4.1            Biostrings_2.64.0      svglite_2.1.0         
[43] xfun_0.32              rvest_1.0.2            lifecycle_1.0.1        pacman_0.5.1           statmod_1.4.36         XML_3.99-0.10         
[49] googlesheets4_1.0.0    zlibbioc_1.42.0        scales_1.2.0           hms_1.1.1              parallel_4.2.1         curl_4.3.2            
[55] memoise_2.0.1          biomaRt_2.52.0         stringi_1.7.8          RSQLite_2.2.15         genefilter_1.78.0      filelock_1.0.2        
[61] rlang_1.0.4            pkgconfig_2.0.3        systemfonts_1.0.4      bitops_1.0-7           evaluate_0.16          lattice_0.20-45       
[67] bit_4.0.4              tidyselect_1.1.2       plyr_1.8.7             magrittr_2.0.3         R6_2.5.1               generics_0.1.3        
[73] DelayedArray_0.22.0    DBI_1.1.3              pillar_1.8.0           haven_2.5.0            withr_2.5.0            survival_3.4-0        
[79] KEGGREST_1.36.3        RCurl_1.98-1.8         modelr_0.1.8           crayon_1.5.1           utf8_1.2.2             BiocFileCache_2.4.0   
[85] tzdb_0.3.0             rmarkdown_2.14         progress_1.2.2         locfit_1.5-9.6         grid_4.2.1             readxl_1.4.0          
[91] blob_1.2.3             reprex_2.0.1           digest_0.6.29          webshot_0.5.3          xtable_1.8-4           munsell_0.5.0         
[97] viridisLite_0.4.0
DEXSeq • 151 views
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Entering edit mode

Thanks for your detail post. I think this might be related to this issue here: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)

Just to verify, could you please post the first lines of your count files?

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1
Entering edit mode

Yes, indeed it is the same error. Here are the first few lines of my count file.

"ENSG00000000003":"001" 0
"ENSG00000000003":"002" 1032
"ENSG00000000003":"003" 412
"ENSG00000000003":"004" 0
"ENSG00000000003":"005" 280
"ENSG00000000003":"006" 263
"ENSG00000000003":"007" 272
"ENSG00000000003":"008" 339
"ENSG00000000003":"009" 295

As already mentioned by Arthur in that thread, I also thought of modifying the count files to remove the quotes around the colon, and that also solves the issue. I tried -

sed -i 's/":"/:/1' countfile
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