[BioC] outlier removal from gene chip

[Weiwei Shi]

my current way is using mahalanobis() distance.

to Sean:
do u think that example: -14k is ok?


On 9/19/06, fhong at salk.edu <fhong at salk.edu> wrote:
> Dear Weiwei,
> The definition of outlier is not clear, and no data point should be
> treated as outlier unless there is reason to believe so. The simple way to
> detect it is that 1.5IQR criteria, which you can write your own code (one
> or two lines). Update me if there are any other method to detect outliers.
>
> Fangxin
>
>
> > dear listers:
> >
> > I have a question on whether bioconductor has some tool-kit to detect
> > outliers and remove them.
> >
> > my original dataset looks like this:
> >             V1       V51       V53        V55       V57
> > 1   -493249600  1.459459 -3.069444  -1.300000  1.935484
> > 2  -1613096495 -1.139269 -5.525281 -16.592593 -1.831978
> > 3   1626196571 -3.500000 -1.011662   2.223881  3.921053
> > 4  -1397009217 -3.571429  1.685714  -1.180297 -6.807692
> > 5   1428659728 -1.405405 -1.469004  -4.779754 -1.033708
> > 6    459853658 -2.158879 -7.510823  -1.085581 -9.382979
> > 7    530182506 -1.431677 -1.336343  -3.126437  4.878788
> > 8   1173842263  1.215385  1.856410  -2.059794 -6.020833
> > 9        28847  2.407895 -2.048889  -1.730337 -1.178947
> > 10 -1961875610  2.864159 -2.301234  -4.733264 -1.172058
> >
> > V1: internal probe id
> > the rests are different samples. the cells are fold-change of
> > disease/normal.
> >
> > summary of the sample columns( V51, ... V57) gives the following:
> >       V51                V53                 V55                V57
> >  Min.   :-482.000   Min.   : -55.7342   Min.   :-122.074   Min.
> > :-14086.750
> >  1st Qu.:  -2.159   1st Qu.:  -1.7312   1st Qu.:  -2.125   1st Qu.:
> > -1.831
> >  Median :  -1.199   Median :  -1.0416   Median :  -1.200   Median :
> > -1.080
> >  Mean   :  -0.918   Mean   :   0.1662   Mean   :  -1.027   Mean   :
> > -1.874
> >  3rd Qu.:   1.441   3rd Qu.:   1.5721   3rd Qu.:   1.419   3rd Qu.:
> > 1.521
> >  Max.   : 198.434   Max.   :1478.1639   Max.   :  95.768   Max.   :
> > 683.519
> >
> >
> > My question is, is there any package which can detect those outliers
> > (like -14086.750)and remove them and get an "average" for each gene
> > (instead of each probe)?
> >
> > Thank you.
> >
> > Weiwei
> >
> > --
> > Weiwei Shi, Ph.D
> > Research Scientist
> > GeneGO, Inc.
> >
> > "Did you always know?"
> > "No, I did not. But I believed..."
> > ---Matrix III
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>
>
> --------------------
> Fangxin Hong  Ph.D.
> Plant Biology Laboratory
> The Salk Institute
> 10010 N. Torrey Pines Rd.
> La Jolla, CA 92037
> E-mail: fhong at salk.edu
> (Phone): 858-453-4100 ext 1105
>
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III