cross platform normalization , can we merge single channel and two channel microarray datasets for analysis.

Question

[sukirtipriya96]

I am working on cross platform normalization, trying to merge single channel and two channel microarray datasets for analysis. Is that possible to merge single channel dataset and two channel dataset? and how to do analysis of two channel dataset like GSE23561.

Answer 1

[Kevin Blighe]

Hi,

I have posted some code for one- and two-colour Agilent arrays here:

• How to process (seems) Agilent microarrry data? (one-colour)
• build the expression matrix step by step from GEO raw data (two-colour)

If you wish to merge these and do analysis on both, you may take some advice that I posted here:

• How to integrate multiple data sets from microarray platform prior meta-analysis?

Kind regards,

Kevin

[sukirtipriya96]

Thank you for your response.

Is that possible to merge one-color with two color microarray dataset of same platform? (cross platform normalization). can we do merge and analyze it. In case of raw file single color and dual color (agilent), different way of normalization to get expression matrix. but in case of series matrix already normalized data, can directly merge and do analysis. is that right?