Hi Jim,

Thanks for your email. I've run mas5 before, but only using default setting. From the help, it does not look like there is a way to specify which reduced set of probes you can use. In addition, from the file, it looks like it has more to do with whether the "object" is read using a reduced set of probes. (I believe if the "object" is read using only the reduced set, mas5 will do the job), so don't know whether it has more to do with the function ReadAffy, but from that, it does not look like it has the option of specifying which reduced set of probes, if we don't use alternative CDF file. Below is the usage of mas5 function. 
mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)
Thanks,

-James

--- On Fri, 8/27/10, James W. MacDonald <jmacdon@med.umich.edu> wrote:

From: James W. MacDonald <jmacdon@med.umich.edu>
Subject: Re: [BioC] question regarding MAS5 normalization with reduced probes
To: "James Anderson" <janderson_net@yahoo.com>
Cc: "bioconductor" <bioconductor@stat.math.ethz.ch>
Date: Friday, August 27, 2010, 10:04 AM

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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-- 
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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