[BioC] options on outputing gene expression based on gene level instead of probe set level for justRMA

[James W. MacDonald]

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 at uw.edu 
> <mailto:jmacdon at 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
>
>                 [[alternative HTML version deleted]]
>
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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