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

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

microarray normalization gene
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updated by Charles Warden Charles Warden • written by fbrundu fbrundu

2 answers

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.

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written by Charles Warden Charles Warden

Which paper shows the need?

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written by Yamol • Yamol

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.

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written by SES SES

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