Dear all,

I am trying to run DESeq2 in R 3.3.1.

When I call library DESeq2 I get this:

"

Loading required package: GenomicRanges
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 objects are masked from ‘package:stats’:

    IQR, mad, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rcpp
Loading required package: RcppArmadillo
Warning messages:
1: multiple methods tables found for ‘fileName’ 
2: multiple methods tables found for ‘organism’"

and when I use " DESeqDataSetFromMatrix" function, I get this error message:

"Error in slot(value, what) : 
  no slot of name "exptData" for this object of class "SummarizedExperiment""

Can u guide me how to solve this problem?

Regards

Nazanin

Usually this is a package version problem. Can you run:

library(BiocInstaller)

biocValid()