Getting gene annotation for a GEO dataset
3
0
Entering edit mode
yuvallb • 0
@yuvallb-13477
Last seen 6.8 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 • 1.4k views
ADD COMMENT
1
Entering edit mode
tcalvo ▴ 90
@tcalvo-12466
Last seen 9 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?

 

ADD COMMENT
0
Entering edit mode
yuvallb • 0
@yuvallb-13477
Last seen 6.8 years ago

Thanks!

I will update here if I find anything

ADD COMMENT
0
Entering edit mode
yuvallb • 0
@yuvallb-13477
Last seen 6.8 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

 

ADD COMMENT

Login before adding your answer.

Traffic: 661 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6