[BioC] how to create an affybatch

[James W. MacDonald]

Hi Sundar,

Venkat Sundar wrote:
> Dear Users, 
> 
> I applied different technical regression LOESS normalization methods ( using GC counts, Tm values,
> XY position etc.,)  on HGU133A data set. 
> Later i mapped back the X,Y
> positions of the probe sequences onto the 712 x 712 intensity matrix. 
> The
> "pm" values later extracted (247965) from the above mapped datais in accordance with those "pm" values actually obtained by using pm function on the affybatch object. ( Just to confirm that i did right)
> 
> Now, I am really having tough time to proceed further in creating an affybatch, summarization methods etc.,
> I tried to construct manually, but lacking proper direction and basics. Can you suggest me for the same to get an initial start.

Sure, look at some code that creates an AffyBatch and emulate that. I 
would suggest read.affybatch().

Best,

Jim


> 
> Meanwhile, i tried the following trick to create an Affybatch. 
> 
> pm(cel.data)<-mynormpm 
> # replacing the "pm values" in the actual affybatch object created by
> using ReadAffy function, with those of the normalized "pm values"
> obtained by                                                            
>         # applying different normalization methods mentioned above. 
> 
> But i still wish to learn creating an affybatch, and performing RMA summarization  manually. 
> 
> with regards,
> Sundar  
> 
> 
>       
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> 
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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.
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734-615-7826