Bioconductor: quantile normalization

Question

[KVC_bioinfo]

Hello All,

I have used Bioconductor ‘preprocessCore’ fro quantile normalization. I am trying t understand how does it work with low expressed or zero count genes. Is someone aware of that?

TIA

Answer 1

[Paolo]

The Wikipedia page for quantile normalization and this answer should provide some light.

[KVC_bioinfo]

Thanks! I have looked them. However, I could not find how it works with low expressed genes.

[Dave Tang]

It's all based on the rank of the gene expression, so lowly expressed genes are ranked lower. If you have a tie in the expression value, it depends on the implementation; you can either take the average or the minimum.