[BioC] outlier removal from gene chip

[Weiwei Shi]

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?"
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