Getting gene annotation for a GEO dataset
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yuvallb • 0
@yuvallb-13477
Last seen 7.4 years ago

I'm trying to read the data of GSE81608 from GEO, but I can't see the gene names. I tried both by reading the CSV file, and by using GOEquery from R. It looks like the gene names are not available. (the CSV just marks the genes by a running number) Is it possible that the dataset was published without the gene names? or am I missing something?

geo • 1.7k views
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tcalvo ▴ 100
@tcalvo-12466
Last seen 17 months ago
Brazil

Well, it seems like the file was badly composed, perhaps. I couldn't get a proper Expression Matrix with GEOquery as well. 

Maybe can you get in touch with the authors?

 

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yuvallb • 0
@yuvallb-13477
Last seen 7.4 years ago

Thanks!

I will update here if I find anything

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yuvallb • 0
@yuvallb-13477
Last seen 7.4 years ago

If this is of interest to anyone, the gene annotation can be found here:

https://s3.amazonaws.com/scrnaseq-public-datasets/manual-data/xin/human_gene_annotation.csv

 

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