Contents
What is LR in edger?
LR = likelihood ratio statistics. PValue = the two-sided p-value. FDR = adjusted p-value.
What is Edge R?
edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability.
How are counts per million calculated?
Here’s how you do it for RPKM: Count up the total reads in a sample and divide that number by 1,000,000 – this is our “per million” scaling factor. Divide the read counts by the “per million” scaling factor.
How to compare the performance of edger and deseq2?
The Euler package venn diagrams are quite easy to make and the areas of the shaded parts are proportional which is a nice touch. I selected 9 genes that were significant with edgeR that were discordant with DESeq2 and created barcharts. Gene9565 in demonstrates that the algorithms deviate in how they treat outliers.
How are genes differentially expressed in DESeq and edger?
In this simple example, DESeq finds 820 genes significantly differentially expressed at FDR<0.05, while edgeR is finds these 820 and an additional 371. Let’s take a look at the detected fold changes from both methods: Here, if genes were found differentially expressed by edgeR only, they’re colored red; if found by both, colored green.
How are DESeq and edger used in RNA Seq?
DESeq and edgeR are two methods and R packages for analyzing quantitative readouts (in the form of counts) from high-throughput experiments such as RNA-seq or ChIP-seq. After alignment, reads are assigned to a feature, where each feature represents a target transcript, in the case of RNA-Seq, or a binding region, in the case of ChIP-Seq.
How to install Edger, deseq2, and eulerr?
To get it to work, clone the repository and open the Rmarkdown (.Rmd) file in Rstudio. You will need to install Bioconductor packages edgeR, DESeq2 and the CRAN package eulerr (for the nifty venn diagrams). Once that’s done you can start working with the Rmd file. For an introduction to Rmd read on here.