Question: For Which Reason Is Useful To Do Gene Wise Normalization In Microarray Matrices?
0
gravatar for fbrundu
5.4 years ago by
fbrundu280
European Union
fbrundu280 wrote:

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

gene normalization microarray • 1.9k views
ADD COMMENTlink modified 5.4 years ago by Charles Warden6.4k • written 5.4 years ago by fbrundu280
2
gravatar for Charles Warden
5.4 years ago by
Charles Warden6.4k
Duarte, CA
Charles Warden6.4k wrote:

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.

ADD COMMENTlink written 5.4 years ago by Charles Warden6.4k
0
gravatar for Yamol
5.4 years ago by
Yamol40
Yamol40 wrote:

Which paper shows the need?

ADD COMMENTlink written 5.4 years ago by Yamol40
1

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.

ADD REPLYlink written 5.4 years ago by SES8.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1144 users visited in the last hour