[BioC] advice on background subtraction/normalization

[Jean Yee Hwa Yang]

Hi Jay,

For within-array normalization, you can use different normalization method 
for different arrays.  Because each adjustment is performed on individual 
arrays and the main aim is to balance the two colors.  The package 
"stepNorm" will do slightly "different" adjustment on different arrays. 
You areable combined marrayNorm object after different within-array 
normalization assuming that these arrays are from similar print-runs. 
Otherwise, care needs to be taken while matching probes.

Cheers

Jean

> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Jay Konieczka
> Sent: Mon 3/19/2007 10:10 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] advice on background subtraction/normalization
>
>
>
> Hi all,
>
> Can someone advise me as to whether or not it's acceptable to use
> different background subtraction methods (or normalization methods)
> for chips within the same marray object (i.e., set of experiments)?
> The reason I ask is that after normalizing my marrayRaw object with
> different background subtraction methods, I compute spatial- and
> intensity-dependent false discovery rates for the marrayNorm object.
> It seems reasonable to me to combine chips from marrayNorm objects
> after doing withinArrayNormalization and prior to doing
> betweenArrayNormalization in order to achieve lower FDRs.  Thoughts?
>
> Cheers,
>
> Jay Konieczka
>
> --
> Jay H. Konieczka
> Ph.D. Student, Antin Lab
> Molecular & Cellular Biology
> University of Arizona
>
> Phone:  1.520.591.3446
>
> 1656 E. Mabel, MRB 317
> Tucson, AZ 85724 USA
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