[BioC] M vs A plot

Wolfgang Huber w.huber at dkfz-heidelberg.de
Tue Feb 10 11:43:26 MET 2004

Hi Richard,

I am not aware of reasons why you shouldn't use a span of more than 0.8. 
Afaik, even values>1 can be useful in some cases (although straight 
robust linear regression (rlm) may be more appropriate in these cases).

On another note, there is a trade-off between what normalization can do 
and data quality - are you sure your funny looking plots are curable by 
normalization, and are not a result of too bad a quality of the data ?

Best wishes

Richard Friedman wrote:

> Dear Sean (Wolfgang, Naomi, and Everybody),
>     The original command that I used was
>  > ira.norm <- maNorm(ira.raw, norm ="p")\
> The command that I used with the altered span is
>  > ira.f8.norm <- maNormMain(ira.raw, f.loc = list(maNormLoess(x = "maA",
> +               y = "maM", z= "maPrintTip", w = NULL, subset =TRUE, span 
> =0.8)),
> +               Mloc = TRUE,  Mscale = TRUE, echo =FALSE)
> This command still gave pronounced curvature at in the middle of one of 
> the printtip blocks and
> at the ends of several printtip blocks.
> I did not use a span greater than .8 because that was counteridicated 
> either in the
> micorarray or loess literature.
> Thank you f all for your suggestion of going to vsn. However,
> as this program is new to me,  I ask if anyone knows a rule of thumb as 
> to how flat the
> printtip loess line should be in order to be acceptable? I would prefer 
> not to change horses
> unless necessary
> Thanks and best wishes,
> Rich
> On Jan 30, 2004, at 2:48 PM, Sean Davis wrote:

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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