[BioC] External expression data/ MAS5 Signal

[Peter Dimitrov]

On Thu, 2002-06-13 at 09:59, Rafael A. Irizarry wrote:
> > #1. how can I import the external expression value table to affy? If
> > possible, in which format?
> what do you mean by external expression value table? if its just a flat 
> file you can use read.table (an R command)
> 
> > #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to
> > calculate the Signal value which is implemented to Microarray Suite version
> > 5 in affy?
> > 
> as far as i know the algorithm isnt public yet so we can't incorporate it.

Can I propose a little change in express, that will accomodate
background specific correction as in the case of MAS5. Specifically,
parameter bg that is used to specify the background adjustment function,
expects only functions that work on a chip or probe pair level, but not
on a probeset level, such as MAS5. The thing is when the data comes to
summary.stat, which is a function working on the probe level, the probe
pairs are already reduced to single number and it is too late to apply
MAS5. For more info look at
http://www.stat.berkeley.edu/users/terry/zarray/Affy/affy_index.html

So, one way to fix this is to have the factor levels used to split the
(globally) adjusted pm's, to be passed as a parameter to bg()(and bgc()
in version 1.1.0), and every other function that doesn't use them, to
use "...".

Thanks,

Peter

> 
> 
> > Thank you very much for the helps in advance.
> > 
> > SW
> > 
> 
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