[BioC] outlier removal from gene chip

[Weiwei Shi]

some added info:
V1 is gene id, but each row represents a probe. so there could be
multiple rows with the same V1 since they (those probes) correspond to
the same gene.

On 9/19/06, Weiwei Shi <helprhelp at gmail.com> wrote:
> 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
>


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

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