DEXSeq unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedIntegerList"’

Question

[ta_awwad]

Dear All, I'm trying to analyze differential exon usage using DEXSeq package. I am getting the following error after running:

dxd = DEXSeqDataSetFromSE( se, design= ~ sample + exon + condition:exon)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedIntegerList"’

any idea what might be wrong? many many thanks sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] biomaRt_2.52.0              GenomicFeatures_1.48.3      DEXSeq_1.42.0               RColorBrewer_1.1-3          AnnotationDbi_1.58.0       
 [6] DESeq2_1.36.0               SummarizedExperiment_1.26.1 GenomicRanges_1.48.0        GenomeInfoDb_1.32.3         IRanges_2.30.0             
[11] S4Vectors_0.34.0            MatrixGenerics_1.8.1        matrixStats_0.62.0          Biobase_2.56.0              BiocGenerics_0.42.0        
[16] BiocParallel_1.30.3        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7             bit64_4.0.5              filelock_1.0.2           progress_1.2.2           httr_1.4.3              
 [6] tools_4.2.0              utf8_1.2.2               R6_2.5.1                 DBI_1.1.3                colorspace_2.0-3        
[11] tidyselect_1.1.2         prettyunits_1.1.1        bit_4.0.4                curl_4.3.2               compiler_4.2.0          
[16] cli_3.3.0                xml2_1.3.3               DelayedArray_0.22.0      rtracklayer_1.56.1       scales_1.2.0            
[21] genefilter_1.78.0        rappdirs_0.3.3           stringr_1.4.0            digest_0.6.29            Rsamtools_2.12.0        
[26] XVector_0.36.0           pkgconfig_2.0.3          dbplyr_2.2.1             fastmap_1.1.0            rlang_1.0.4             
[31] rstudioapi_0.13          RSQLite_2.2.15           BiocIO_1.6.0             generics_0.1.3           hwriter_1.3.2.1         
[36] dplyr_1.0.9              RCurl_1.98-1.8           magrittr_2.0.3           GenomeInfoDbData_1.2.8   Matrix_1.4-1            
[41] Rcpp_1.0.9               munsell_0.5.0            fansi_1.0.3              lifecycle_1.0.1          stringi_1.7.8           
[46] yaml_2.3.5               zlibbioc_1.42.0          BiocFileCache_2.4.0      grid_4.2.0               blob_1.2.3              
[51] parallel_4.2.0           crayon_1.5.1             lattice_0.20-45          Biostrings_2.64.0        splines_4.2.0           
[56] annotate_1.74.0          hms_1.1.1                KEGGREST_1.36.3          locfit_1.5-9.6           pillar_1.8.0            
[61] rjson_0.2.21             geneplotter_1.74.0       codetools_0.2-18         XML_3.99-0.10            glue_1.6.2              
[66] BiocManager_1.30.18      png_0.1-7                vctrs_0.4.1              gtable_0.3.0             purrr_0.3.4             
[71] assertthat_0.2.1         cachem_1.0.6             ggplot2_3.3.6            xtable_1.8-4             restfulr_0.0.15         
[76] survival_3.4-0           tibble_3.1.8             GenomicAlignments_1.32.1 memoise_2.0.1            statmod_1.4.37          
[81] ellipsis_0.3.2  

[ATpoint]

class(se)?

[ta_awwad]

Hi Alex,

thanks for your reply.

> class (se)
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"

[ta_awwad]

> traceback()
11: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
        sQuote(fdef@generic), sQuote(cnames)), domain = NA)
10: (function (classes, fdef, mtable) 
    {
        methods <- .findInheritedMethods(classes, fdef, mtable)
        if (length(methods) == 1L) 
            return(methods[[1L]])
        else if (length(methods) == 0L) {
            cnames <- paste0("\"", vapply(classes, as.character, 
                ""), "\"", collapse = ", ")
            stop(gettextf("unable to find an inherited method for function %s for signature %s", 
                sQuote(fdef@generic), sQuote(cnames)), domain = NA)
        }
        else stop("Internal error in finding inherited methods; didn't return a unique method", 
            domain = NA)
    })(list(structure("CompressedIntegerList", package = "IRanges")), 
        new("standardGeneric", .Data = function (i, x, exact = TRUE, 
            strict.upper.bound = TRUE, allow.NAs = FALSE) 
        standardGeneric("NSBS"), generic = structure("NSBS", package = "S4Vectors"), 
            package = "S4Vectors", group = list(), valueClass = character(0), 
            signature = "i", default = NULL, skeleton = (function (i, 
                x, exact = TRUE, strict.upper.bound = TRUE, allow.NAs = FALSE) 
     ...
9: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, 
       allow.NAs = allow.NAs)
8: normalizeSingleBracketSubscript(i, x, allow.NAs = TRUE, as.NSBS = TRUE)
7: extractROWS(x, i)
6: extractROWS(x, i)
5: x@elementMetadata[i, , drop = FALSE]
4: x@elementMetadata[i, , drop = FALSE]
3: SE[order(mcols(SE)$gene_id), ]
2: SE[order(mcols(SE)$gene_id), ]
1: DEXSeqDataSetFromSE(se, design = ~sample + exon + condition:exon)

[ta_awwad]

Hi Alex,

any idea how to solve this error?

Thanks

TA

[PK]

Mee too....any suggestions? I could not find the answer