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RMA background correction normalization only

Hi,

Does the RMA method for background correction and normalization (not summarization) give log2 transformed intensities? or which step gives log transformed values?

Thank you in advance, Good luck in your studies

rma
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updated by Ram Ram • written by akutasame • akutasame

I really need an answer, please make a comment if you have an idea.

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written by akutasame • akutasame

Are you using the expresso function in the "affy" Bioconductor package? I believe in that one, the log2 transformation is done as part of the RMA summarization step (also in medianpolish), and not in the previous steps. But, you could always check what the output looks like to make sure.

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updated by Ram Ram • written by Jason Chen • Jason Chen

1 answer

The RMA method by definition produces log [base 2] (log2) intensities. The steps are:

  1. background correction
  2. quantile normalisation
  3. log2 transformation

Summarisation at the probe or probe-set level can be controlled via the target parameter that is passed to the rma() function. Depending on the array type, a probe-set may encompass a single gene or a single exon. Try it out yourself.

Kevin

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written by Kevin Blighe Kevin Blighe

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