[BioC] question regarding MAS5 normalization with reduced probes

[James W. MacDonald]

Hi James,

On 8/26/2010 1:05 PM, James Anderson wrote:
> Hi,
>
> I am trying to use MAS5 to normalize some cel files with reduced set
> of probes (some probes whose PM is not significantly higher than MM
> is filtered), does anyone know how to do this? Does that require
> creating a new CDF file?

Have you tried running mas5() from the affy package? Having never tried, 
I don't know, but it seems a simple enough test.

If you do need to create a new cdf, you will want to use the affxparser 
package.

Best,

Jim


>
> thanks a bunch,
>
> -James
>
>
>
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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