Downloading RNAseq datasets from GEO into R

Question

[Alana]

Well, I'm new to all this (first year of my master's degree)... I have fourteen GEO datasets to analyze. I was trying to download them into R, but I was using the wrong strategy (GEOquery for RNAseq data. Seriously?!). I still need some expression data and I don't know how to start. Can anyone shed some light on this?

Answer 1

[ATpoint]

Indeed GEOquery cannot give you the actual data as it could (given availability) for microarrays. Often authors of the study upload some sort of raw or normalized counts under "Supplement" in the GEO entry. If not you can check whether projects such as recount or BioJupies have the raw counts available. If not you need to download the fastq files and process manually.

For more details please elaborate more.

[Alana]

thank you!

Answer 2

[Trivas]

I would look into GEO2R https://www.ncbi.nlm.nih.gov/geo/geo2r/

[ATpoint]

Unless they updated this recently, this only supports arrays.

[Trivas]

It's a new-ish Beta feature as of last year. Not all datasets are available yet, but many of the newer ones are.

[ATpoint]

Cool, I did not know: https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html#rnaseq

[Alana]

thank you all

Answer 3

[alserg]

You can check out our package phantasusLite. Not all RNA-seq datasets are available there, but it's a good percent. See the vignette here for the example: https://bioconductor.org/packages/release/bioc/vignettes/phantasusLite/inst/doc/phantasusLite-tutorial.html#loading-precomputed-rna-seq-counts

Also, if you're interested in human RNA-seq datasets, there is some efforts from GEO side to quantify RNA-seqs: https://www.ncbi.nlm.nih.gov/geo/info/rnaseqcounts.html I'm not aware of any R package wrapping this, but it should be relatively straightforward to download.