NCBI Geo Database & GEOQuery
 

I am trying to analyze the gene expression data from NCBI GEO website
xttp://xxx.ncbi.nlm.nih.gov/geo/
(Please replace xxx by www and xttp by http)

locally. I have downloaded the GDS SOFT format files and am using GEOquery/BioConductor tool to query them.
I want to find list of all the genes specifically upregulated in a particular disease.

I don't want to use the E-utils or any remote utilities for this.

Any help is appreciated.