For Which Reason Is Useful To Do Gene Wise Normalization In Microarray Matrices?

Question

[fbrundu]

Hi all,

I am quite sure that column normalization can be used to make all chips vary in the same range (correct me if I am wrong). Anyway I cannot understand row wise normalization (probe wise). Why is it used and for which purpose?

Thanks

Answer 1

[Charles Warden]

The main example I can think of is for visualization: when creating heatmaps, most software will give you an option to "standardize" your data (set mean to 0, sd =1 for each gene / probe / isoform). This way, genes in the up-regulated group are generally colored red (or whatever color you choose), regardless of absolute intensity / expression.

In general, I would say you are right: most "normalization" steps focus on making expression values between chips / samples most comparable.

Answer 2

[Yamol]

Which paper shows the need?

[SES]

Hi Yamol, this is not an answer. Please make this a comment so that you can get clarification and the post can be updated. That will help people answer the question.