Thanks Evan,
I am working on Illumina arrays and, if possible, I'll try also SCAN and
fRMA as you recommend.
I used to think that normalization has to be done after batch effects
removal, in order not to flatten the signal. I use loess normalization
after ComBat for this particular reason.
>From your experience the order in which normalization and batch effects
removal are done is not important?
Thanks

~Francesco Brundu


On 10 October 2013 16:57, Johnson, William Evan <wej@bu.edu> wrote:

>  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@gmail.com 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
>
>
>

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