Loading a dataset via acession number

Question

[angus.j.g.campbell]

I am trying to load this data set: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA251582

I have installed GEOquerry a while back. When i run the following code I get this result:

library(GEOquery)
eset <- getGEO("PRJNA251582", getGPL = FALSE)


> eset <- getGEO("PRJNA251582", getGPL = FALSE)
Error in file.exists(destfile) : object 'destfile' not found

Also what is the difference betwen calling eset <- getGEO("PRJNA251582", getGPL = FALSE) and eset <- getGEO("PRJNA251582", getGPL = FALSE)[[1]] ?

Answer 1

[ATpoint]

This is RNA-seq, not microarrays which GEOquery assumes, so it is expected that it produces no output. RNA-seq is sequencing data, you therefore will need to download the fastq files, align/quantify to get a matrix of raw counts.

For starters maybe this paper: https://peerj.com/preprints/27283/

Please also search biostars and the web for RNA-seq processing tutorials.

For downloading the files (if you really want to do that), search sra-explorer.info for the dataset to get download links. Beside that, there are plenty of posts and tutorials on how to download and process RNA-seq data, please use the search function.