[BioC] M vs A plot

Richard Friedman friedman at cancercenter.columbia.edu
Tue Feb 10 15:37:25 MET 2004

Dear Wolfgang,

	I thought that span was the fraction of points used in the smoothing 
and had a theoretical maximum of 1. I also thought that it was not a 
good idea to use all the points in the smoothing, lest the more extreme 
points dominate.	

	As for data quality, the slides are quite dirty with an uneven 
background. I used Spot to read the slides to compensate for background 
variability, Spot irregularity, and stains as much as possible. However 
the non-flattening of curve may still be a data quality problem. Also, 
shouldn't the dependence on total intensity (A) be removed?

	Anyway, I will try higher span values and try successive fits later 
today. I will also try the 2D option. Unless you think that  what I 
have described is such that flattening will not help. I can send you  a 
copy of all of the printtip curves and the worst printtip curve if you 
are willing to look at them.

Thanks and best wishes,

On Feb 10, 2004, at 5:43 AM, Wolfgang Huber wrote:

> 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
>   Wolfgang
> 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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