R programmin RNA seq

Question

[sehriban.buyukkilic]

Hi everyone, I'm trying to use edgeR for DE, but I could't install edger in R, I'm using MacBook Air Catalina. Which version of R best for my Mac and also including edgeR and DESeq2? Is anyone have idea about that? Thank you so much. kindly

[bkleiboeker]

Install latest version of R for macOS (make sure to select correct version for intel or apple silicone, aka m1/m2), then install latest version of RStudio for macOS, then in the console run:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("edgeR")

Which I got from: https://bioconductor.org/packages/release/bioc/html/edgeR.html

[barslmn]

In which steps did you encounter problems? A good way of installing/updating packages is my using a package manager. You can use something like brew in macOS to manage your packages.

[sehriban.buyukkilic]

when ı try to load edgeR package, the come true. Actually I did all this step, I used brew, biomanager. I deleted R and reinstall on Mac, its still the same.

[sehriban.buyukkilic]

Error: package or namespace load failed for ‘edgeR’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘locfit

this is error

[barslmn]

There is probably a missing build dependency. Try working your way up to dependencies. Install missing R packages one by one e.g install.packages("locfit") and post the error messages.

[sehriban.buyukkilic]

install.packages("locfit") Warning in install.packages : package ‘locfit’ is not available (for R version 3.5.2)

this error come true

Answer 1

[Gordon Smyth]

The error message that you show (Error: ... there is no package called locfit) would arise when you try to load edgeR library(edgeR). This shows that you have in fact successfully installed edgeR itself but haven't installed edgeR's dependencies. If you check back to the page https://bioconductor.org/packages/edgeR/, you will see that edgeR imports locfit and Rcpp. If you don't have those packages installed already then you need:

library("BiocManager")
install("locfit")
install("Rcpp")
install("edgeR")

then you will be able to load edgeR. You will need to have limma installed as well but the error message suggests you have that already.

It is typical for Bioconductor packages to have dependencies and edgeR has fewer than most. You'll need to go through this process of installing the other packages that they depend on for any Bioconductor package that you want to work with.