[BioC] M vs A plot

[Wolfgang Huber]

Hi Richard

loess normalization has a parameter "span", which determines the 
so-called bandwidth of the smoothing window. Apparently the default is 
too small for you (leading to a too flexible regression curve), so you 
have to make it larger.

There is a lot of literature on choosing bandwidths (most of it seems to 
involve some kind of cross-validation), but I am actually not aware on 
recommendations for microarrays other than "by eye".

Best wishes
  Wolfgang

-- 
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Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber
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Richard Friedman wrote:
> Mick,
> 
> 	Thanks for the help. What concerns  me however is not a single
> point being an outlier, but the whole loess fit to all the points leading
> the lowess curve for a few printips to deviate significantly from being
> a straight line practically colinear with the x-axis (abcissa). The two
> test cases on which I learned to use marray - the apoE data that comes
> with spot, and the swirl data that comes with marray, all had
> significantly expressed genes - however they also had flat normalized
> lowess curves. Significant curvature in the lowess curve leads me
> to be concerned that the spots associated with that region of
> the curve are improperly normalized.
> 
> 	Can anyone out there give me:
> 
> 1. Guidelines as to how flat the lowess curve should be for the
>    data to be considered normalized.
> 
> 2. Advice as to what to do if the printtip normalization option
>    in marray did not remove intensity dependence.
> 
> If anyone is willing to look at the M vs A curve, I would be grateful.
> 
> Thanks and best wishes,
> Rich
> 
> 
>