[BioC] 3 questions about Affy: expresso()

[Rafael A. Irizarry]

On Tue, 7 Oct 2003, James MacDonald wrote:

> 1. To my knowledge, no and no.

fit.li.wong, the function expresso calls, has an option
remove.outliers
by default its TRUE. you want to make it FALSE.
you can do this via the summary.param argument in expresso as explained in
the help page.


> 2. To do this you would have to hack the sources to return the row
> medians from medianpolish.
> 3.
> http://www.bioconductor.org/repository/devel/package/Source//affy_1.3.19.tar.gz
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> <adumas at ucla.edu> 10/06/03 09:33PM >>>
> Hi all!
> 
>   1. How about Outlier detection in Li-Wong model ?
>       Does expresso() automatically include this procedure ?
>       Or  Is there anyway I can turn on/off  ?
> 
>   2. Is it possible to get measures of probe affinity effect(probe
> pattern) 
> in RMA model?
> 
>   3. Where can I download  C or R source code for RMA ?
> 
> Thank you a lot in advance,
> best
> MyungShin Oh
> 
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