[BioC] question regarding MAS5 normalization with reduced probes

[James W. MacDonald]

Hi James,

I misunderstood your question. I thought you already had a reduced set 
of probes you wanted to run mas5() on.

So yeah, if you want to use a reduced set of probes you could use some 
code written by Ariel Chernomoretz (and modified by Jenny Drnevitch) 
that has been posted and referenced many times on this list:

https://stat.ethz.ch/pipermail/bioconductor/2006-September/014242.html

Alternatively, you could play with the affxparser package, which has the 
capability (IIRC) to do the same.

Best,

Jim



On 8/30/2010 10:29 AM, James Anderson wrote:
> 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 at med.umich.edu>
> wrote:
>
> From: James W. MacDonald<jmacdon at med.umich.edu> Subject: Re: [BioC]
> question regarding MAS5 normalization with reduced probes To: "James
> Anderson"<janderson_net at yahoo.com> Cc:
> "bioconductor"<bioconductor at 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
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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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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