Entering edit mode
I have a bunch of 2000 arrays I want to normalize with rma() from affy
package. Then from time to time there will be single arrays to be
analyzed together with these 2000. To apply the same normalization
procedure to the single arrays later I want to split the rma step in
its
elements.
bg.correct(data, method="rma")
As it's array wise I think no problem for the single array.
normalize(data, method="quantiles")
I think here I need to save the mean values for each row to normalize
the single array later with this values (I know it's not totally exact
but I think acceptable). In my understanding of the quantile
normalization the sorted perfect match values should be exactly the
same
for every sample, but I got differences.
So my questions are:
1. How does the last step look to got exactly the same results as with
rma()
2. Why the differences in quantile normalization?
3. Is there a better way to handle this task?
Any help would be appreciated,
Christian