This function provides a wrapper to run DESeq for differential expression analysis. It includes two steps,
a matrix containing read counts for each gene, can be the output of
the sample classification labels.
A CountDataSet object with size factors and dispersion parameters been estimated.
Xi Wang, [email protected]
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data, Genome Biol, 11, R106.
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Loading required package: Biobase 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, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: doParallel Loading required package: foreach Loading required package: iterators Loading required package: DESeq Loading required package: locfit locfit 1.5-9.1 2013-03-22 Loading required package: lattice Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating to 'DESeq2'. Warning message: In .local(object, ...) : in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates. Warning message: system call failed: Cannot allocate memory
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