[BioC] External expression data/ MAS5 Signal

Rafael A. Irizarry rafa@jhu.edu
Mon, 17 Jun 2002 09:31:03 -0400 (EDT)

also keep in mind that rma return log2(expression). if you want to make 
a direct comp you should look at 2^exprs(express(Plob))

rma and li and dchip with no pm only give similar results. i think the 
average correlation is about .9 (on the log scale). for mas 5.0 its around .8.

Mon, 17 Jun 2002, Laurent Gautier wrote:

> On Thu, Jun 13, 2002 at 02:04:50PM -0400, Sek Won Kong, M.D. wrote:
> (...)
> > 
> > I wondered there's quite a difference in calculated expression values from
> > AvgDiff, AvgDiff2, li.wong and rma. Previous I used invariant set normalized
> > MAS 5 signal values for analysis. However when I tried to implement the
> > quantile normalization and rma, there's big differences in reults ( I mean
> > the final results the list of genes ). So I wondered the why, and wanted to
> > compare 5 different kinds of expression algorithms.
> The 'because' that answers the 'why' is probably linked with the fact that
> the methods are fairly different (see their respective description in the
> help pages)...
> You may want to look at the individual probe sets for the genes for which
> the results are very different. (try the function get.PPset)... do not
> hesitate to give us feedback about the differences observed.
> > 
> > And could you let me know how to calculate the PM-only model of Li-Wong in
> > affy? li.wong seems like PM-MM model.
> >
> In the package, we consider that PMs and MMs probe intensities are used
> to compute 'adjusted' probe intensities. In the case of PMs-MMs,
> it can be thought of subtracting the noise to the signal.
> The parameter 'bg' for express or 'bg.correct' for generateExprSet
> (for Plob and Cel.container respectively) let you specify how to
> get the 'adjusted' values.
> The function 'bg.correct.pmonly' returns only the PMs and can be
> used...
> regards,
> Laurent