[BioC] genefilter (nsFilter function)

[Jenny Drnevich]

>
>The IQR is the inter-quartile range, which is the difference between 
>the 75th and 25th percentile of your data. It is a more robust 
>measure of the range of the data, as it will not be affected by a 
>small number of extreme values (unlike, say the variance).

I've always been a little suspicious of filtering on IQR or other 
measures of variance, and I just came upon a case where filtering on 
IQR could exclude some genes of interest. I have a 2 trt x 4 time 
point experiment, and the control treatment is not expected to change 
over time. Any genes that only change at only 1 or 2 time points in 
the infected treatment could show a low IQR and be filtered out. So 
be careful of your filtering criteria when you have a complex 
experimental design!

Cheers,
Jenny





>Best,
>
>Jim
>
>
>>
>>iqr <- function(x) IQR(x) > 2.5
>>filter <- nsFilter(eset, var.filter=TRUE, var.func = iqr, 
>>var.cutoff = 0.5)    regards
>>Anne
>>
>>         [[alternative HTML version deleted]]
>>
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>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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e-mail: drnevich at illinois.edu