Retrieve gene from GEO/ArrayExpress datasets
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.
• 1,363 views
•
link
written
by
boczniak767
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Discrepancy in GEO2R vs. Raw Data Analysis: Significance of DEGs
written by Saeedeh Salehi •
-
How to deal with duplicate gene symbol from GEO databse
written by Emily •
-
Get GEO microarray probe sequences by GPL ID
written by predeus
-
How to amalgamate gene expressions grouped by UNIPROT?
written by james •
-
Ideas for integrating transcriptomic data/co-expression network and genome-scale metabolic networks
written by pixie@bioinfo
-
How to map Arabidopsis reference ids to locus id for the newer arrays
written by anc.informatics •
-
scRNA-seq, filter low expressed genes based on RPKM value
written by chipolino •
-
How to design matrix for LIMMA between control and stress conditions to calculate logFC and p-value.
written by asnanizami •
-
Merging expression data from multiple platforms
written by mforde84
-
Finding differentially expressed probesets from a single microarray experiment.
written by siddharth.avadhanam •
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.