[BioC] Utilizing outlier information in RMA and MAS estimation?

[Laurent Gautier]

The handling of NAs in not implemented for all the processing methods,
unfortunately. We had some discussions about that around the
first release, agreed that it would be cool to have it for all,
but ... it never went top priority since few appear to use the
feature (or may be few do so 'cause it's not working in every case).
Other may correct me, I think that skipping the background correction
for now should make it through (for mas, may be for rma too).
If you really-really-really what it to work and come with a fix,
it would be neat too...

Sorry, not much more to suggest for now...



Hopin' it helps,



Laurent





On Wed, Jul 16, 2003 at 02:35:05PM -0500, Lishuang Shen wrote:
> Hi:
> 
> With ReadAffy, Affy can mask the outliers as NA with option: rm.outlier=TRUE.
> 
> But I could not do RMA or MAS 5 estimation with AffyBatch obtained in this way. 
> either using rma or using expresso, as I always got the error message about 
> NA/NaN:
> 
> >background correction: mas 
> >PM/MM correction : mas 
> >expression values: mas 
> >background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign 
> function call (arg 1)
> 
> Has anyone used outlier information during the expression estimation? I 
> searched all the mailing list archieve, but found no mention on if this 
> information is use or not, or information on if outliers marked as NA allowed 
> in estimation.
> 
> 
> Thank you for your time.
> 
> 
> Lishuang Shen
> 
> BarleyBase,
> Iowa State University
> Ames, Iowa 50010
> Tel: (515)-294-8479 (Office
> Email: lshen at iastate.edu; shen_lishuang at yahoo.com
> 
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