Question: eUtils and GEO database
0
gravatar for russhh
2.5 years ago by
russhh4.6k
UK, U. Glasgow
russhh4.6k wrote:

Hi I'm trying to use NCBI::eUtils to obtain microarray / RNASeq datasets from GEO for use in a meta-analysis. I've based my searches on the examples at https://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html

I've a couple of simple questions: Say I start with this query (from the FAQ):

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? ... 

db=gds& ...

term=GPL96[ACCN]+AND+gse[ETYP]+AND+cel[suppFile]& ...

retmax=5000& ...

usehistory=y

How do I filter to remove "SuperSeries" from the returned datasets?

How do I filter to keep only datasets with at least 4 samples and less than 200 samples?

Ta

eutils ncbi geo • 825 views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.5 years ago by russhh4.6k
1

Following command would help exclude SuperSeries but not sure about the filter based on the number of samples.

esearch -db gds -query "GPL96[ACCN] AND gse[ETYP] AND cel[suppFile] NOT SuperSeries"
ADD REPLYlink written 2.5 years ago by Sej Modha4.3k
1

thanks, I was trying to use "... AND (NOT SuperSeries)". I enjoyed your nextgenbug yesterday, regards

ADD REPLYlink written 2.5 years ago by russhh4.6k
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