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Question: DESeq2 library loading error
0
gravatar for smartdogs4chris
4 weeks ago by
smartdogs4chris0 wrote:

I configured DESeq2 onto my R Studio (Version 1.0.136 – © 2009-2016 RStudio, Inc. Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_3) AppleWebKit/604.5.6 (KHTML, like Gecko) using:

 

##DESeq2
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
browseVignettes("DESeq2")
source("https://bioconductor.org/biocLite.R")
biocLite("data.table")

From there I loaded the library backapge DESeq2. 

 library("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:limma’:

    plotMA

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

    IQR, mad, sd, var, xtabs

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

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums,
    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, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians

Attaching package: ‘DelayedArray’

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘stringi’ 1.1.5 is being loaded, but >= 1.1.7 is required

 

However, whenever I go to run the first step, I get this error. 

> dds <- DESeqDataSetFromMatrix(countData = mouse.df1,
+                               colData = group,
+                               design = ~ condition)
Error in DESeqDataSetFromMatrix(countData = mouse.df1, colData = group,  : 
  could not find function "DESeqDataSetFromMatrix"

 

Can someone please walk me through how to correct this? I'm new to DESeq2. 

 
ADD COMMENTlink modified 4 weeks ago by Michael Love18k • written 4 weeks ago by smartdogs4chris0
0
gravatar for Michael Love
4 weeks ago by
Michael Love18k
United States
Michael Love18k wrote:

The error says you did not successfully load DESeq2 so there’s no point trying to use the package functions. You should try installing the library that needs updating.

Error: package or namespace load failed for ‘DESeq2’
ADD COMMENTlink written 4 weeks ago by Michael Love18k

I'll just add: be sure to follow the instructions at www.bioconductor.org/install and use biocLite() to update your packages and to install new ones, including those from CRAN. Using any other method of installing and updating packages, such as install.packages() or RStudio's menus, introduces risk of dependency problems.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Levi Waldron600
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