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.