Limit of quantile normalization

Question

Is quantile normalization adequate for normalizing data with very few samples?

For example this microarray data. Typically after normalization we'd like to compare Cancer-1 with Normal and Cancer-2 with Normal for differential expression.

    mRNA     Cancer-Type-1   Cancer-Type-2  Normal
    -----------------------------------------------------------
    mRNA1      30        49    12
    mRNA2     199        200   78
    ...        ...       ...  ....
    mRNA1000   13        40    88

If not what is the appropriate normalization method?

score 1 · Accepted Answer · answered Jan 28 '13 at 11:31

1

Quantile normalization works well when the samples are comparable (ie have a high correlation). We don't know whether that is the case with your data. There is nothing in the algorithm that requires a large number of arrays, but realistically with only 3 arrays your analysis is pretty limited no matter what the normalization method.

answered Jan 28 '13 at 11:31

Leo Schalkwyk

166
2

Thanks. Why "high correlation" is needed? Any reference for that? – neversaint Feb 02 '13 at 12:07

Limit of quantile normalization

1 Answers1