Question: RMA background correction normalization only
0
gravatar for akutasame
5.0 years ago by
akutasame40
United Kingdom
akutasame40 wrote:

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

myposts • 2.5k views
ADD COMMENTlink modified 20 months ago by Kevin Blighe67k • written 5.0 years ago by akutasame40

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

ADD REPLYlink written 5.0 years ago by akutasame40

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.

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by Jason Chen20

Nope, I am doing probe level Anova, I did RMA background correction and quantile normalization only, I did not do summarization. But I just found that RMA background correction is taking log2 base raw intensities. http://www.plexdb.org/modules/documentation/RMAexplained.pdf

Thank you for your comment

ADD REPLYlink written 5.0 years ago by akutasame40
2
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

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

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

Summarising over exons (probe-sets) or genes can be controlled via the target parameter that is passed to the rma() function.

Kevin

ADD COMMENTlink written 20 months ago by Kevin Blighe67k
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