Retrieve gene from GEO/ArrayExpress datasets
0
0
Entering edit mode
5.2 years ago
boczniak767 ▴ 870

Is there any way to retrieve expression values for a given gene from GEO and ArrayExpress?

The aim is to check if a given gene was expressed in stress conditions in a plant. I imagine I could use gene or probe ID.

I know there are R packages like GEOquery but it doesn't do what I need.

databses • 1.0k views
ADD COMMENT
0
Entering edit mode

The thing is that arrays offer relative measures so it only shows if a gene is differentially-expressed, not if it is expressed at all. There is the GEO2R option (https://www.ncbi.nlm.nih.gov/geo/geo2r/) for array data that allow a simple and quick comparison between samples of a given dataset to give you a first hint. For anything else I guess you have to download RNA-seq data as this can give information about expression levels rather than a binary statement of DEG/non-DEG.

ADD REPLY

Login before adding your answer.

Traffic: 1292 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