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Data mining for 300 genes from GEO

Hi All,

I have a gene list of ~ 300 genes. I want to get from GEO all the high-throughput expression studies for these genes. I can write a R script to make this search with GEOsearch package. But I guess the package only allows for geneid/name based search. I was wondering if there is a way to search based on advanced options, e.g. get only expression data where the sample source is root.

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updated by Biostar Biostar • written by GR GR

1 answer

I think you could a local Blastx program on the 300 amino acid sequences, and parse the gene IDs to a list to use with your GEOsearch.

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written by theobroma22 theobroma22

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