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.

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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