[BioC] Save rma normalization results for later use

[Laurent Gatto]

Dear Christian,

I think that there are two packages that implement this approach. One is 
'RefPlus', available in Bioconductor. There is also fRMA (frozen RMA) from 
Rafael Irizarry and Matthew McCall, but I don't know if it is available yet. 

Hope this helps.

Laurent

On Tuesday 17 February 2009 14:20:55 Christian Ruckert wrote:
> 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
>
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