How to get gene expression value from Arrayexpress

ArrayExpress has a wonderful R package for data search, download and analysis but it doesn't always work in perfection. Therefore it always good to have an alternative to download the raw data/CEL and analyze it. This R script will simply take the accession number in command line argument and save the expression data in a file named as  Gene_expression.txt.
How to download expression data set from NCBI GEO HERE

Prerequisite 


We need the following R libraries to run the script
  • ArrayExpress 
  • aff

Uses 


Rscript script_name accession_number

Limitations 

  • This script is written specifically for Arabidopsis data sets, therefore, you have to modify it as per your requirement. 

Script 




Was This Post Useful?

Add This To Del.icio.us Share on Facebook StumbleUpon This Add to Technorati Share on Twitter
Labels: ,

No comments:

Post a Comment

Have Problem ?? Drop a comments here!

Subscribe to: Post Comments (Atom)