On Fri, Nov 4, 2011 at 10:26 AM, Richard Friedman <
friedman@cancercenter.columbia.edu> wrote:

>
> On Nov 2, 2011, at 10:16 AM, Vincent Carey wrote:
>
>  you can read about formally calibrated outlier assessment for microarrays
>> in
>>
>> http://bioinformatics.**oxfordjournals.org/content/25/**1/48<http://bioinformatics.oxfordjournals.org/content/25/1/48>
>>
>
> Dear Vincent and List,
>
>        I read your paper with great interest. i will implement it for
> datasets for Affymetrix Chips with
> mismatch probes, to which it is geared, along with the weighting method
> suggested by Jim MacDonald, for arrays which pass the test. However a Gene
> ST1.0 dataset has come up with this kind of rejection question. Has you
> method be adapted to Gene ST1.0 arrays? If not, do you know of
> a method analogous to yours which can be used for ST1.0s.
>

There is a fair amount of generality in arrayMvout but it has not all been
exercised to the same degree.  The simplest uses work from affyBatch or
lumiBatch instances and compute QA statistics tailored to the respective
platforms.  If you have a data frame of array-specific QA statistics for
some other platform, arrayOutliers() will perform calibrated multivariate
outlier detection with these measures.  For the early affy arrays, NUSE and
RLE statistics from affyPLM play a role; I don't know if these are readily
computed for 1.0 ST arrays at this time.  arrayMvout uses
Mahalanobis-distance based procedures, but the distance is robustified by
inward peeling to deal with masking problems that can arise with multiple
outliers.

Let's not forget the  Bioconductor mdqc package, which also deals with a
differently robustified Mahalanobis distance for this purpose.


>
> Thanks and best wishes,
> Rich
> ------------------------------**-----------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu>
> http://cancercenter.columbia.**edu/~friedman/<http://cancercenter.columbia.edu/%7Efriedman/>
>
> I am a Bayesian. When I see a multiple-choice question on a test and I
> don't
> know the answer I say "eeney-meaney-miney-moe".
>
> Rose Friedman, Age 14
>
>
>
>
>
>
>> On Wed, Nov 2, 2011 at 10:04 AM, Richard Friedman <friedman@cancercenter.
>> **columbia.edu <friedman@cancercenter.columbia.edu>> wrote:
>> Dear Bioconductor List,
>>
>>       Does anyone know of an objective criterion for the identification
>> of outlying arrays
>> by pca?
>>
>>       I usually do this subjectively. However the experimental
>> investigator whom I am helping
>> has a different subjective sense than I do, so that I wonder if there is
>> a hard-and-fast criterion.
>>
>>
>
>
> -
>
>
>
>
>
>
>

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