DESeq2 1.6 mcols error
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ipurusho • 0
@ipurusho-6881
Last seen 9.5 years ago
United States

Hi ,

 

I recently installed the latest version of DESeq2 (VERSION 1.6.0) and upon running the command DESeq(dds), I receive the following error:

 

Error in ncol(mcols(dds)) :

  error in evaluating the argument 'x' in selecting a method for function 'ncol': Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘mcols’ for signature ‘"DESeqDataSet"’

 

Is this a bug? I was using v1.4 where the same code was working, and upon switching to 1.6 I receive the error above.

 

Thanks in advance.

Immanuel

deseq2 bug • 5.6k views
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Can you edit your question to provide the output of sessionInfo() after you get this error, please?

Did you upgrade your entire "bioconductor stack" to 3.0?

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Yes, I'd agree with Steve.

See instructions for upgrading all packages here: "Upgrading installed Bioconductor packages"

http://www.bioconductor.org/install/#update-bioconductor-packages

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eva.knig • 0
@evaknig-7114
Last seen 9.3 years ago
France

Hello,

I get the same error as Immanuel, and I think I have the most recent version of Bioconductor (3.1.1) and DESeq2 (1.6.2). However I get some warnings when I import DESeq2. I am running R version 3.1.1. Below you find all information on my session. Thanks alot. Eva

 

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help

> require("DESeq2")
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

Loading required package: IRanges

Attaching package: ‘IRanges’

The following objects are masked from ‘package:S4Vectors’:

    aggregate.Rle, as.data.frame.DataFrame, as.data.frame.Rle,
    as.data.frame.Vector, as.env, as.list.List, as.list.Rle,
    as.list.SimpleList, .Call2, classNameForDisplay, compare,
    countMatches, countQueryHits, countSubjectHits, DataFrame,
    diff.Rle, duplicated.DataTable, duplicated.Rle, duplicated.Vector,
    elementLengths, elementMetadata, elementMetadata<-, elementType,
    endoapply, findMatches, findRun, fixedColumnNames, fold,
    get_showHeadLines, get_showTailLines, isConstant, isEmpty,
    isSingleInteger, isSingleNumber, isSingleNumberOrNA,
    isSingleString, isSingleStringOrNA, isTRUEorFALSE, levels.Rle,
    List, mcols, mcols<-, mean.Rle, median.Rle, mendoapply, metadata,
    metadata<-, new2, nrun, phead, ptail, quantile.Rle, queryHits,
    queryLength, recycleIntegerArg, recycleNumericArg, remapHits,
    rename, revElements, rev.Rle, Rle, runLength, runLength<-, runmean,
    runq, runsum, runValue, runValue<-, runwtsum, safeExplode,
    selfmatch, setMethods, setValidity2, shiftApply, showAsCell,
    SimpleList, sort.Rle, sort.Vector, strsplitAsListOfIntegerVectors,
    subjectHits, subjectLength, summary.Rle, svn.time, unique.Rle,
    unique.Vector, unstrsplit, values, values<-, width

The following objects are masked from ‘package:BiocGenerics’:

    end<-, start<-, width, width<-

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rcpp
Loading required package: RcppArmadillo
There were 50 or more warnings (use warnings() to see the first 50)

> warnings()
Warning messages:
1: multiple methods tables found for ‘width’
2: multiple methods tables found for ‘start<-’
3: multiple methods tables found for ‘width<-’
4: multiple methods tables found for ‘end<-’
5: multiple methods tables found for ‘unsplit’
6: replacing previous import by ‘IRanges::end<-’ when loading ‘GenomicRanges’
7: replacing previous import by ‘IRanges::start<-’ when loading ‘GenomicRanges’
8: replacing previous import by ‘IRanges::unsplit’ when loading ‘GenomicRanges’
9: replacing previous import by ‘IRanges::width’ when loading ‘GenomicRanges’
10: replacing previous import by ‘IRanges::width<-’ when loading ‘GenomicRanges’
11: replacing previous import by ‘IRanges::end<-’ when loading ‘XVector’
12: replacing previous import by ‘IRanges::start<-’ when loading ‘XVector’
13: replacing previous import by ‘IRanges::unsplit’ when loading ‘XVector’
14: replacing previous import by ‘IRanges::width’ when loading ‘XVector’
15: replacing previous import by ‘IRanges::width<-’ when loading ‘XVector’
16: multiple methods tables found for ‘width’
17: multiple methods tables found for ‘width’
18: multiple methods tables found for ‘start<-’
19: multiple methods tables found for ‘width<-’
20: multiple methods tables found for ‘end<-’
21: replacing previous import by ‘GenomicRanges::end<-’ when loading ‘DESeq2’
22: replacing previous import by ‘GenomicRanges::start<-’ when loading ‘DESeq2’
23: replacing previous import by ‘GenomicRanges::width’ when loading ‘DESeq2’
24: replacing previous import by ‘GenomicRanges::width<-’ when loading ‘DESeq2’
25: replacing previous import by ‘IRanges::unsplit’ when loading ‘DESeq2’
26: replacing previous import by ‘S4Vectors::aggregate.Rle’ when loading ‘DESeq2’
27: replacing previous import by ‘S4Vectors::as.data.frame.DataFrame’ when loading ‘DESeq2’
28: replacing previous import by ‘S4Vectors::as.data.frame.Rle’ when loading ‘DESeq2’
29: replacing previous import by ‘S4Vectors::as.data.frame.Vector’ when loading ‘DESeq2’
30: replacing previous import by ‘S4Vectors::as.env’ when loading ‘DESeq2’
31: replacing previous import by ‘S4Vectors::as.list.List’ when loading ‘DESeq2’
32: replacing previous import by ‘S4Vectors::as.list.Rle’ when loading ‘DESeq2’
33: replacing previous import by ‘S4Vectors::as.list.SimpleList’ when loading ‘DESeq2’
34: replacing previous import by ‘S4Vectors::.Call2’ when loading ‘DESeq2’
35: replacing previous import by ‘S4Vectors::.__C__Annotated’ when loading ‘DESeq2’
36: replacing previous import by ‘S4Vectors::.__C__characterORNULL’ when loading ‘DESeq2’
37: replacing previous import by ‘S4Vectors::.__C__DataFrame’ when loading ‘DESeq2’
38: replacing previous import by ‘S4Vectors::.__C__DataTable’ when loading ‘DESeq2’
39: replacing previous import by ‘S4Vectors::.__C__DataTableORNULL’ when loading ‘DESeq2’
40: replacing previous import by ‘S4Vectors::.__C__Hits’ when loading ‘DESeq2’
41: replacing previous import by ‘S4Vectors::classNameForDisplay’ when loading ‘DESeq2’
42: replacing previous import by ‘S4Vectors::.__C__List’ when loading ‘DESeq2’
43: replacing previous import by ‘S4Vectors::compare’ when loading ‘DESeq2’
44: replacing previous import by ‘S4Vectors::countMatches’ when loading ‘DESeq2’
45: replacing previous import by ‘S4Vectors::countQueryHits’ when loading ‘DESeq2’
46: replacing previous import by ‘S4Vectors::countSubjectHits’ when loading ‘DESeq2’
47: replacing previous import by ‘S4Vectors::.__C__Rle’ when loading ‘DESeq2’
48: replacing previous import by ‘S4Vectors::.__C__SimpleList’ when loading ‘DESeq2’
49: replacing previous import by ‘S4Vectors::.__C__Vector’ when loading ‘DESeq2’
50: replacing previous import by ‘S4Vectors::DataFrame’ when loading ‘DESeq2’

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] DESeq2_1.6.2              RcppArmadillo_0.4.550.1.0
[3] Rcpp_0.11.3               GenomicRanges_1.16.4     
[5] GenomeInfoDb_1.0.2        IRanges_1.22.10          
[7] S4Vectors_0.4.0           BiocGenerics_0.12.1      

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.44.0      AnnotationDbi_1.28.1
 [4] base64enc_0.1-2      BatchJobs_1.5        BBmisc_1.8          
 [7] Biobase_2.24.0       BiocParallel_1.0.0   brew_1.0-6          
[10] checkmate_1.5.0      cluster_1.15.3       codetools_0.2-9     
[13] colorspace_1.2-4     DBI_0.3.1            digest_0.6.4        
[16] fail_1.2             foreach_1.4.2        foreign_0.8-61      
[19] Formula_1.1-1        genefilter_1.46.1    geneplotter_1.44.0  
[22] ggplot2_1.0.0        grid_3.1.1           gtable_0.1.2        
[25] Hmisc_3.14-6         iterators_1.0.7      lattice_0.20-29     
[28] latticeExtra_0.6-26  locfit_1.5-9.1       MASS_7.3-34         
[31] munsell_0.4.2        nnet_7.3-8           plyr_1.8.1          
[34] proto_0.3-10         RColorBrewer_1.0-5   reshape2_1.4        
[37] rpart_4.1-8          RSQLite_1.0.0        scales_0.2.4        
[40] sendmailR_1.2-1      splines_3.1.1        stringr_0.6.2       
[43] survival_2.37-7      tools_3.1.1          XML_3.96-1.1        
[46] xtable_1.7-1         XVector_0.4.0       

> dds <- makeExampleDESeqDataSet(n=12)
Error in ncol(mcols(dds)) :
  error in evaluating the argument 'x' in selecting a method for function 'ncol': Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘mcols’ for signature ‘"DESeqDataSet"’

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0
Entering edit mode

hi Eva,

Similar to our advice for Immanuel, you have a mix of up-to-date Bioconductor packages, and out of date Bioconductor packages, which is bound to cause problems. Here are the updating instructions: http://bioconductor.org/install/#update-bioconductor-packages . You should make sure to update all out of date packages.

You have GenomicRanges 1.16, while the current release is 1.18

You have IRanges 1.22 while the current release is 2.0

However, you also have current DESeq2 (1.6).

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Also, here is some advice on why to use library() instead of require() in scripts: http://yihui.name/en/2014/07/library-vs-require/

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eva.knig • 0
@evaknig-7114
Last seen 9.3 years ago
France

Hi Michael,

thank you for your quick answer. In your answer to Immanuel I missed that you recommened to update all packages. Now everything works fine. Sorry for missing that before.

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