normalizeCyclicLoess function in limma may help. But I don't know whether it
is publicly available now. It will be in new version of Bioconductor.
See, http://bioconductor.org/packages/2.6/bioc/manuals/limma/man/limma.pdf
More array weights should be given to the control probes as you may consider
they are constant across arrays.
As the author siad normalise.loess may be another option.
Cheers,
Di


On Sun, Jul 11, 2010 at 1:26 AM, Kamila Naxerova
<naxerova@fas.harvard.edu>wrote:

> Dear list,
>
> I was searching the archives for discussions about the Affymetrix miRNA
> chip... there are only a few threads and most of them  are almost a year
> old. I was wondering whether in the meantime people had gathered some
> experience with analysis strategies - normalization in particular - and were
> willing to share some insights. I do not feel comfortable using RMA because
> I doubt that total miRNA expression can be assumed to be constant across
> samples (particularly when studying developmental processes or cancer). Has
> anybody played with the options?
>
> Thanks!
> Kamila
>
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