How To Download Dataset For The Microarray Data Analysis From Ncbi For Affymetrix ?

Question

[Arpitha Hebbar]

Hello,

How to download affymetrix microarray data (cancer data compared with normal data should contain maximum of 4 samples) from the ncbi? And how the data input file should be? I'm using R program limma package in windows for the analysis purpose. Please help.

Answer 1

[Sean Davis]

The GEOquery bioconductor package is specifically designed to solve this problem:

http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

[Arpitha Hebbar]

cant i use limma package for GEO datasets ?

[Sean Davis]

Of course. GEOquery simply gets the data into R. Once the data are in R, you can use any R-based workflow or tool that you like.