I am studying about how to do normalization. At first, I think that people have to calculate the log2 ratio as a primary step to convert the T=R/G ratio in microarray into another simple number to show the difference of up and down regulated of the genes, but then I see that in some case, people do log2 transformation as a step of normalization. So, is it log2 transformation a normalization method? Is it log2 transformation the same as log2 ratio calculation? (or they are different?
Thank you for your attention. Please ask me if my question confuse you!
Taking log2 is a transformation, not a normalization.
Normalizations make the distributions more similar. They can be applied to untransformed or to transformed data (the choice is not arbitrary; it depends on the kind of normalization what makes sense).
Note that log(R/G) = log(R) - log(G).
In dual-color hybridizations, a frequently used normalization is the lowess-normalization that actually detrends the log(R/G) against the log(R*G) data. It therefore makes sense to calculate log(R/G) first and then normalize.
Thank you a lot for your answers. I have successfully do normalization with my test data today. But I now wonder do we have any validation methods after doing normalization?
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