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!
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written
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maya123z •
1 answer
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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