[BioC] M vs A plot

[Richard Friedman]

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:

> Richard,
>
> The print-tip-loess lines should (I think) be straight and on the 
> x-axis
> (y=0) after print-tip-normalization.  If that isn't the case, perhaps 
> you
> could post exactly the commands you used to do your normalization.  
> That may
> help people determine better what is going on.
>
> In reference to ridding you of intensity-dependent variability,
> loess-normalization is designed to locally center the data but does 
> not, in
> itself, deal with the variability that may be intensity-dependent.  
> For that
> problem, you may need to look into something like vsn or other scaling
> method.
>
> Sean
>
>
> On 1/30/04 2:35 PM, "Richard Friedman" 
> <friedman at cancercenter.columbia.edu>
> 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
>>
>>
>>
>> On Fri, 30 Jan 2004, michael watson (IAH-C) wrote:
>>
>>> Richard
>>>
>>> The nature of any normalisation means that we will always have 
>>> outliers -
>>> those spots that deviate from all the rest.  There could be two 
>>> reasons -
>>> that spot represents a differentially expressed gene or the spot is
>>> unreliable and comes from a "bad" spot.
>>>
>>> I'd take the common sense approach to these outliers:
>>>
>>> i) Check any replicate spots - if all replicate spots are outliers 
>>> then you
>>> have evidence that it's a differentially expressed gene.  However, 
>>> if the
>>> replicates disagree, this is evidence that the outlier comes from an
>>> unreliable / bad measurement
>>>
>>> ii) Go take a look at the spot on the original image.  Does it look 
>>> "good"?
>>>
>>> You are likely always to find outliers after normalisation.  This 
>>> is, after
>>> all, what we are looking for, isn't it?  The key is to be able to 
>>> say, when
>>> you see an outlier, if that spot is of reliable quality or not.
>>>
>>> Thanks
>>> Mick
>>>
>>> -----Original Message-----
>>> From: Richard Friedman [mailto:friedman at cancercenter.columbia.edu]
>>> Sent: 29 January 2004 22:26
>>> To: 'Bioconductor Mail List'
>>> Cc: IRA A TABAS
>>> Subject: [BioC] M vs A plot
>>>
>>>
>>> Dear Bioconductors,
>>>
>>> I have normalized a series of arrays using print-tip normalization.
>>> Where as the systematic error in the unnormalized data was 
>>> pronounced,
>>> The systematic error on the normalized array was reduced greatly.
>>> The M vs. A curve was flat for most of the 48 print-tips. However 
>>> for a
>>> few
>>> printips, for A>12 M deviates from close to zero. in one case, M 
>>> rises
>>> as high
>>> as M=1/2. at A=15. This only involves a small fraction of the spots 
>>> (It
>>> is hard to
>>> estimate what proportion).
>>>
>>> Does this sound serious?
>>>
>>> If so, what should I do about it?
>>>
>>> Is anyone willing to look at the JPEg file (I did not attach it
>>> because I don't
>>> know if I am allowed to do so).
>>>
>>> Thanks and best wishes,
>>> Rich
>>> ------------------------------------------------------------
>>> Richard A. Friedman, PhD
>>> Associate Research Scientist
>>> Herbert Irving Comprehensive Cancer Center
>>> Oncoinformatics Core
>>> Lecturer
>>> Department of Biomedical Informatics
>>> Box 95, Room 130BB or P&S 1-420C
>>> Columbia University Medical Center
>>> 630 W. 168th St.
>>> New York, NY 10032
>>> (212)305-6901 (5-6901) (voice)
>>> friedman at cancercenter.columbia.edu
>>> http://cancercenter.columbia.edu/~friedman/
>>>
>>> "Spring, Summer, and Winter.
>>> Then Fall came along,
>>> and that's the end of our song,
>>> and the pigeons never hibernate at all".
>>> -Rose Friedman, age 7
>>> (These are the correct lyrics and supersede
>>> the version previously at the end of my sig)
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>>>
>>
>> ------------------------------------------------------------
>> Richard A. Friedman, PhD
>> Associate Research Scientist
>> Herbert Irving Comprehensive Cancer Center
>> Oncoinformatics Core
>> Lecturer
>> Department of Biomedical Informatics
>> Box 95, Room 130BB or P&S 1-420C
>> Columbia University Medical Center
>> 630 W. 168th St.
>> New York, NY 10032
>> (212)305-6901 (5-6901) (voice)
>> friedman at cancercenter.columbia.edu
>> http://cancercenter.columbia.edu/~friedman/
>>
>> "Spring, Summer, and Winter.
>> Then Fall came along,
>> and that's the end of our song,
>> and the pigeons never hibernate at all".
>> -Rose Friedman, age 7
>> (These are the correct lyrics and supersede
>> the version previously at the end of my sig)
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>>
>