Hi Fong(?).
On Sat, Jul 24, 2010 at 2:10 AM, Fong <fongchunc...@gmail.com> wrote:
> Hi,
>
> I've used aroma.affymetrix to generate and extract the probeset
> summaries (chip effects) from a set of Human Exon array samples I
> have. And then performed batch adjustment on these probeset summaries
> using another R script (ComBat.R). Now I got the adjusted probeset
> values and I was running whether it was possible to feed these into
> firma again to use?
>
> I can't figure out how to load external RMA data into the
> aroma.affymetrix package,
Unfortunately, there is no such option available in aroma.affymetrix.
It can be done, but you really have to dig into the low-level parts
which requires lots of knowledge, which only a few developers have.
What adds to the complications, is that the FIRMA model relies on the
residuals of the probe-level modelling (PLM), see the bottom equation
in column 2 page 2 of Purdom et al. (2008):
r_ijk = y_ijk + c_i + p_k
where {y} are the probe signals, {c} are the estimated chip effects
and {p} the estimate probe affinities. With the risk of making a fool
of myself, I think ComBat is correcting only the chip effects {c}.
This means that when calculating the above residuals you would use
ComBat-normalized chip effects but the default RMA probe affinities.
I don't think FIRMA algorithm was designed for this. Have you though
about this?
/Henrik
>
> Any help would be greatly appreciated.
>
> --
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>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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