Tag: dgelist

DGE from tumor-adjacent normal pair RNA-seq data. For an individual, no replicate

Single sample analysis can be done in edgeR, while it is deprecated in DNASeq2 in 2018 probably (if you can use old DESeq version then it will work in single sample also). For egdeR you just do library(edgeR) setwd() rawdata <- read.delim(“filename”, check.names=FALSE, stringsAsFactors=FALSE) ngenes <- 10000 #no. of genes…

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keep only genes expressed in sample at the same time as a particular gene of interest

Filter DGElist object: keep only genes expressed in sample at the same time as a particular gene of interest 0 Hello, need some help here as I’m kind of stuck with the edgeR DGElist format. I have a DGE list named x with the following dimensions: > dim(x ) [1]…

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Calculate fold change in edgeR with one sample per condition

Hi, We have run a pilot RNA-Seq study with one sample per condition, this is just a test run. I understand there is no valid statistical test in this case, however just curious to obtain differential expression through edgeR package in R assuming dispersion = 0.4 for the human data….

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