[BioC] M vs A plot

Richard Friedman friedman at cancercenter.columbia.edu
Mon Feb 9 22:45:15 MET 2004

Dear Wolfgang and Everybody,

	I tried the span as high as .8 but it didn't cure the dip in the 
curve. I believe that higher
than .8 is not recommended (I saw this in either the microarray or the 
Loess literature, I am
not sure which

Thanks and best wishes,

On Jan 30, 2004, at 2:48 PM, Wolfgang Huber wrote:

> 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
> -- 
> -------------------------------------
> 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
> -------------------------------------
> 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

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