Question: DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
0
gravatar for bruce.hayward
4 months ago by
bruce.hayward0 wrote:

I'm getting an error message while trying to perform a DEXSeq analysis. The libraries and commands I entered worked correctly a couple of years ago on an earlier R/Bioconductor build. The current R and Bioconductor packages were freshly installed a few days ago. The data consists of a set of indexed bam files and a descriptor text file containing two columns: Name and Type. The data are analysed without a problem by DESeq2.

The commands leading to the error code:

> library("Rsamtools")
> library(TxDb.Mmusculus.UCSC.mm10.knownGene)
> library(org.Mm.eg.db)
> library("GenomicAlignments")
> library("DEXSeq")
> library("annotate")
> sampleTable <- read.table("bamlist_WT-Dutch.txt", header=T, sep="\t")
> bamlist <- file.path(sampleTable$Name)
> bamfiles <- BamFileList(bamlist, yieldSize=2000000)
> sampleTableCsv <- read.csv("bamlist_WT-Dutch.txt", header=T, sep="\t")
> exonicParts <- disjointExons(TxDb.Mmusculus.UCSC.mm10.knownGene)
> exonCounts <- summarizeOverlaps(exonicParts, reads=bamfiles, mode="Union", singleEnd=F, ignore.strand=T, inter.feature=F)
> colData(exonCounts) <- DataFrame(sampleTableCsv)
> exonCounts$Type <- relevel(exonCounts$Type, "WT")
> dxdDataSet <- DEXSeqDataSetFromSE(exonCounts, design= ~Name + exon + Type:exon)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘NSBS’ for signature ‘"CompressedIntegerList"’


> 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("CompressedIntegerList"), new("standardGeneric", .Data = function (i, 
        x, exact = TRUE, strict.upper.bound = TRUE, allow.NAs = FALSE) 
    standardGeneric("NSBS"), generic = "NSBS", package = "S4Vectors", 
        group = list(), valueClass = character(0), signature = "i", 
        default = NULL, skeleton = (function (i, x, exact = TRUE, 
            strict.upper.bound = TRUE, allow.NAs = FALSE) 
        stop("invalid call in method dispatch to 'NSBS' (no default method)", 
            domain = NA))(i, x, exact, strict.upper.bound, allow.NAs)), 
        <environment>)
9: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, 
       allow.NAs = allow.NAs)
8: normalizeSingleBracketSubscript(i, x, exact = FALSE, 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(exonCounts, design = ~Name + exon + Type:exon)



> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] annotate_1.62.0                         
 [2] XML_3.98-1.20                           
 [3] DEXSeq_1.30.0                           
 [4] RColorBrewer_1.1-2                      
 [5] DESeq2_1.24.0                           
 [6] GenomicAlignments_1.20.1                
 [7] SummarizedExperiment_1.14.0             
 [8] DelayedArray_0.10.0                     
 [9] BiocParallel_1.18.0                     
[10] matrixStats_0.54.0                      
[11] org.Mm.eg.db_3.8.2                      
[12] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7
[13] GenomicFeatures_1.36.4                  
[14] AnnotationDbi_1.46.0                    
[15] Biobase_2.44.0                          
[16] Rsamtools_2.0.0                         
[17] Biostrings_2.52.0                       
[18] XVector_0.24.0                          
[19] GenomicRanges_1.36.0                    
[20] GenomeInfoDb_1.20.0                     
[21] IRanges_2.18.1                          
[22] S4Vectors_0.22.0                        
[23] BiocGenerics_0.30.0                     

loaded via a namespace (and not attached):
 [1] httr_1.4.0             bit64_0.9-7            splines_3.6.1         
 [4] Formula_1.2-3          assertthat_0.2.1       statmod_1.4.32        
 [7] latticeExtra_0.6-28    blob_1.2.0             GenomeInfoDbData_1.2.1
[10] progress_1.2.2         pillar_1.4.2           RSQLite_2.1.1         
[13] backports_1.1.4        lattice_0.20-38        digest_0.6.20         
[16] checkmate_1.9.4        colorspace_1.4-1       htmltools_0.3.6       
[19] Matrix_1.2-17          pkgconfig_2.0.2        biomaRt_2.40.3        
[22] genefilter_1.66.0      zlibbioc_1.30.0        xtable_1.8-4          
[25] scales_1.0.0           tibble_2.1.3           htmlTable_1.13.1      
[28] ggplot2_3.2.0          nnet_7.3-12            lazyeval_0.2.2        
[31] survival_2.44-1.1      magrittr_1.5           crayon_1.3.4          
[34] memoise_1.1.0          hwriter_1.3.2          foreign_0.8-71        
[37] data.table_1.12.2      tools_3.6.1            prettyunits_1.0.2     
[40] hms_0.5.0              stringr_1.4.0          locfit_1.5-9.1        
[43] munsell_0.5.0          cluster_2.1.0          compiler_3.6.1        
[46] rlang_0.4.0            grid_3.6.1             RCurl_1.95-4.12       
[49] rstudioapi_0.10        htmlwidgets_1.3        bitops_1.0-6          
[52] base64enc_0.1-3        gtable_0.3.0           DBI_1.0.0             
[55] R6_2.4.0               gridExtra_2.3          knitr_1.23            
[58] rtracklayer_1.44.2     bit_1.1-14             zeallot_0.1.0         
[61] Hmisc_4.2-0            stringi_1.4.3          Rcpp_1.0.1            
[64] geneplotter_1.62.0     vctrs_0.2.0            rpart_4.1-15          
[67] acepack_1.4.1          xfun_0.8
dexseq • 186 views
ADD COMMENTlink written 4 months ago by bruce.hayward0

I'd guess that you have packages that are not current or are from different releases. What does

BiocManager::valid()

say? Can you address issues it might identify?

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 24k
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