How to extract data from GEO datasets using GEOparse?
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2.0 years ago
maya123z ▴ 60

I'm trying to extract RNAseq data in Python using the GEOparse package. I used the following code:

import GEOparse
gse = GEOparse.get_GEO(geo="GSE84422", destdir="./")
data = gse.table

However, I get an error: "AttributeError: 'GSE' object has no attribute 'table'". The package documentation says that table should be a standard attribute of GSE objects (see section 3.3.2). I've been trying to follow this tutorial. Any advice greatly appreciated!

python geo GEOparse RNASeq • 3.1k views
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Entering edit mode
22 months ago
ichbinlynn93 ▴ 30

Just noticed this question until recently working on it.

The tutorial use GDS instead of GSE where GSE is a series of samples but GDS usually refers to a pre-defined dataset.

So for GSE:

You may get all the GSMS (samples) information using:

gse.phenotype_data

Then you can use the sample name to retrieve the corresponding data, for example:

gse.gsms['GSM26805'].table

If you want to know how to annotate it, first you need to get the platform information:

gse.gpls

In my case, I got GPL8300, then what needs to be finished is:

gse.gpls['GPL8300'].table

You may need to merge the tables after extracting all the data. Hope it works!

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