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Venkat Sundar
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30
@venkat-sundar-3560
Last seen 10.3 years ago
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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