[BioC] M vs A plot
w.huber at dkfz-heidelberg.de
Tue Feb 10 11:43:26 MET 2004
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 ?
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
> + 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,
> On Jan 30, 2004, at 2:48 PM, Sean Davis wrote:
Division of Molecular Genome Analysis
German Cancer Research Center
Phone: +49 6221 424709
Fax: +49 6221 42524709
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