Thanks, Jim. That's very helpful.

-Jack

On Thu, Mar 7, 2013 at 8:57 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Please don't take things off list.
>
> On 3/6/2013 7:59 PM, Jack Luo wrote:
>
>> Gene 1.0 ST.
>>
>
> At this point I guess I need to know what you mean by gene level. The affy
> package by definition only summarizes at the transcript level. But that
> doesn't mean that you only have one probeset per gene, as there may still
> be duplicates (splice variants or whatnot). If you just want a single
> expression value per gene, you can either use the genefilter package to
> subset by Entrez ID, or you could alternatively use one of the MBNI
> re-mapped cdf packages.
>
> Best,
>
> Jim
>
>
>
>> On Wed, Mar 6, 2013 at 2:53 PM, James W. MacDonald <jmacdon@uw.edu<mailto:
>> jmacdon@uw.edu>> wrote:
>>
>>     Hi Jack,
>>
>>
>>     On 3/6/2013 11:48 AM, Jack Luo wrote:
>>
>>         Hi,
>>
>>         I am trying to RMA normalize a bunch of cel files and output
>>         the gene
>>
>>
>>     A bunch of cel files of what Array type?
>>
>>
>>         expression matrix to gene level (instead of probe set level),
>>         is there any
>>         option in justRMA that can do this (or any other function that
>>         can do
>>         this?) I searched the options on justRMA, does not seem to
>>         have this
>>         option.
>>
>>         Thanks,
>>
>>         -Jack
>>
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>>
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>>
>>     --     James W. MacDonald, M.S.
>>     Biostatistician
>>     University of Washington
>>     Environmental and Occupational Health Sciences
>>     4225 Roosevelt Way NE, # 100
>>     Seattle WA 98105-6099
>>
>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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