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Question: DESeq2 error when creating the DESeqDataSet
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gravatar for sebastian.lobentanzer
19 months ago by
sebastian.lobentanzer10 wrote:

I am trying to create a DESeqDataSet from a SummarizedExperiment. I am getting the error message:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assayNames’ for signature ‘"DESeqDataSet"’

While researching, I found this (verified) example to test with:

df=data.frame("treat"=sample(c(80:100),6, replace=FALSE),
              "treat1"=sample(c(90:103),6, replace=FALSE),
              "treat2"=sample(c(80:100),6, replace=FALSE),
              "ctrl"=sample(c(60:90),6, replace=FALSE),
              "ctrl1"=sample(c(60:90),6, replace=FALSE),
              "ctrl2"=sample(c(60:90),6, replace=FALSE))
conds<-as.factor(c("Treat","Treat","Treat","Control","Control","Control"))
coldata <- data.frame(row.names=colnames(df), conds)
dds=DESeqDataSetFromMatrix(countData=df,colData=coldata,design=~conds)

Unfortunately, this example gives the same error. I tried the "airway" example, same thing happenend. My sessionInfo() is:

R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

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 methods base

other attached packages: [1] DESeq2_1.10.1
RcppArmadillo_0.7.500.0.0 Rcpp_0.12.7
SummarizedExperiment_1.4.0 Biobase_2.34.0
GenomicRanges_1.26.1 [7] GenomeInfoDb_1.10.0
IRanges_2.8.0 S4Vectors_0.12.0
BiocInstaller_1.20.3 AnnotationHub_2.2.5
BiocGenerics_0.20.0

loaded via a namespace (and not attached): [1] locfit_1.5-9.1
lattice_0.20-34 Rsamtools_1.26.1
Biostrings_2.42.0 digest_0.6.10 [6] mime_0.5 R6_2.2.0 plyr_1.8.4
chron_2.3-47 acepack_1.4.1 [11] ShortRead_1.28.0 RSQLite_1.0.0 httr_1.2.1
ggplot2_2.1.0 zlibbioc_1.20.0 [16] GenomicFeatures_1.26.0 data.table_1.9.6
annotate_1.48.0 rpart_4.1-10
Matrix_1.2-7.1 [21] splines_3.3.1
BiocParallel_1.8.0 geneplotter_1.48.0
stringr_1.1.0 foreign_0.8-67 [26] RCurl_1.95-4.8 biomaRt_2.30.0
munsell_0.4.3 shiny_0.14.2 httpuv_1.3.3 [31] rtracklayer_1.34.0 htmltools_0.3.5
nnet_7.3-12 gridExtra_2.2.1
htmlTable_1.7 [36] interactiveDisplayBase_1.8.0 Hmisc_4.0-0 XML_3.98-1.4
GenomicAlignments_1.10.0 bitops_1.0-6 [41] grid_3.3.1 xtable_1.8-2 gtable_0.2.0 DBI_0.5-1 magrittr_1.5 [46] scales_0.4.0 stringi_1.1.2
XVector_0.14.0 hwriter_1.3.2
genefilter_1.52.1 [51] latticeExtra_0.6-28
Formula_1.2-1 RColorBrewer_1.1-2 tools_3.3.1 survival_2.40-1 [56] AnnotationDbi_1.36.0
colorspace_1.2-7 cluster_2.0.5 knitr_1.14

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("DESeqDataSet"), function (x, ...) standardGeneric("assayNames"), ) 
9: assayNames(object) 
8: "counts" %in% assayNames(object) 
7: validityMethod(object) 
6: anyStrings(validityMethod(object)) 
5: validObject(.Object) 
4: initialize(value, ...) 
3: initialize(value, ...) 
2: new("DESeqDataSet", se, design = design) 
1: DESeqDataSet(se, design = ~cell + dex)
ADD COMMENTlink modified 19 months ago • written 19 months ago by sebastian.lobentanzer10
2
gravatar for sebastian.lobentanzer
19 months ago by
sebastian.lobentanzer10 wrote:

Solution: I recompiled all Bioconductor packages with

source("https://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs, type="source")

and then restarted.

ADD COMMENTlink written 19 months ago by sebastian.lobentanzer10
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