Question

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

0

Entering edit mode

11.3 years ago

Arpitha Hebbar ▴ 210

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.

ncbi microarray limma affymetrix • 5.6k views

ADD COMMENT • link updated 21 months ago by Ram 44k • written 11.3 years ago by Arpitha Hebbar ▴ 210

score 1 · Answer 1 · 2013-09-24

1

Entering edit mode

11.3 years ago

Sean Davis 27k

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

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

ADD COMMENT • link 11.3 years ago by Sean Davis 27k

0

Entering edit mode

cant i use limma package for GEO datasets ?

ADD REPLY • link 11.3 years ago by Arpitha Hebbar ▴ 210

1

Entering edit mode

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.

ADD REPLY • link 11.3 years ago by Sean Davis 27k