error in "DESeqDataSetFromMatrix" function in DESeq2

Question

[nazaninhoseinkhan]

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

[russhh]

Hi, the first part of the output is just the startup message. That's not an error, and can be ignored - indeed, you can suppress it using suppressPackageStartupMessages(library(DESeq2)). Could you post the precise code that you used when you called DESeqDataSetFromMatrix, please. The call should look like DESeqDataSetFromMatrix(my_counts, my_samples, some_model_equation)

[nazaninhoseinkhan]

Hi, Thanks for the reply. Here is my code:

setwd("C:\Users\Administrator\Desktop\DESeqInput")

cts<-read.table("cts.txt", header=TRUE, row.names=1)

coldata<-read.table("coldata.txt", header=TRUE, row.names=1)

coldata <- coldata[,c("condition","type")]

dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)

[Kevin Blighe]

Has this problem since been resolved? Restarting your computer and then starting a fresh R session and/or re-installing the package can sometimes mitigate these errors. It's good to close your R session after you use it each time in order to prevent errors with namespace, which are frequent, given the amount of packages that now exist. Otherwise, please post the output of sessionInfo().

[nazaninhoseinkhan]

Hi Kevin, Thanks. Yes, my problem was resolved. I installed R 3.5 and then installed all packages from BioClite.