0 down vote favorite I have very limited experience in R but would like to know if anyone can share their pipeline for analyzing GSE files from GEO, both for microarray and/or RNA-seq. The eventual goal would be to look at the differentially expressed genes.
For example, I would like to analyze GSE113590 which is a RNA-seq data and GSE47045 which is a microarray data.
The general consensus seems to be that you download the data using this:
source("http://bioconductor.org/biocLite.R") biocLite("GEOquery") library("GEOquery") gset <- getGEO("GSE113590", GSEMatrix =TRUE)
But I'm not sure how to move forward from here, and there seems to be a different pipeline depending on whether it is a microarray / RNA-seq.
Thanks for your help.