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Bioconductor: quantile normalization

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

normalization biocinductor
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updated by Paolo Paolo • written by KVC_bioinfo KVC_bioinfo

1 answer

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

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written by Paolo Paolo

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

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written by KVC_bioinfo KVC_bioinfo

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.

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written by Dave Tang Dave Tang

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