Hi Jim,

Thanks a lot for the link. I've tried the code in the link, it works without any problem if I were to take the whole probesets out. However, I do encounter some problem when I need to take not only some probe sets, but also some probes (but not the whole probe set) out, maybe because I did not provide the correct format of the probes. 

(I assume you are familiar with the content in the script provided in the link). 

If I randomly take out 2000 probe sets from U133A, 
maskedprobeSets = rownames(MAS5_matrix)[sample(1:22283,2000)]
RemoveProbes(listOutProbes=NULL, listOutProbeSets=maskedprobeSets, cleancdf)

It works fine and whatever affyBatch object read using the cleancdf has a reduced dimension. 

However, if I do 

maskedprobeSets = rownames(MAS5_matrix)[sample(1:22283,2000)]
maskedprobes = rownames(pm(A))[1:2000]
RemoveProbes(listOutProbes=maskedprobes, listOutProbeSets=maskedprobeSets, cleancdf)

The error msg shows as:
Error in get(pset[i], env = get(cdfpackagename)) : 
  object '315997at' not found

Do you know what is the correct format of the input for the probes (not probe sets) to be taken out? 



Thanks a lot,


-James


--- On Mon, 8/30/10, 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: Monday, August 30, 2010, 12:25 PM

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@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
>>
>>
>>
>>
>> [[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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