Johnson, William Evan | 10 Oct 16:57 2013

Re: Normalization before ComBat

Hi Francesco,

If I understand your question correctly: Normalization removes background, probe and sample effects.
Often batch effects are often unaddressed by normalization. In contrast, most batch adjustment methods
do not address probe and background effects--so both tools are needed for some datasets. For
normalization (for Affy arrays) we strongly recommend either SCAN or fRMA for normalization.

In terms of distortion, yes there is a chance that the signal could be a little distorted by normalization
and/or batch adjustment. Yes, a normalization method that addresses batch at the same time might be a
little less likely to cause signal distortion. However in practice, a two-step normalization/batch
adjustment works just fine.

Hope this helps.

Evan

On Oct 10, 2013, at 5:17 AM,
francesco.brundu@...<mailto:francesco.brundu@...> wrote:

Hi all,
I have a question about running combat on microarray data.
In http://biostatistics.oxfordjournals.org/content/8/1/118.full it is said that (3.1) 'We assume
that the data have been normalized' before batch correction.
My question is, what is intended here as normalization? Does not normalization before batch correction
distort the signal?
Thanks

~Francesco Brundu

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@...
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


Gmane