[BioC] Filter over group averages

[Wolfgang Huber]

Michael

it is not difficult to write such a function, using "split" on your 
covariates, and then "lapply" and "rowMeans" on the resulting list of 
sets of arrays.

The reason such a function does not exist in genefilter is that this 
type of filtering disturbs the null distribution of subsequently used 
t-statistics or F-statistics that are commonly used in per-gene 
hypothesis testing, and thus typically leads to invalid p-values. See 
the man page of the "nsFilter" (and the reference cited therein, which 
will appear soon).

If you don't do hypothesis testing afterwards, i.e. if you use this 
filtering as a variable selection step e.g. for classification, 
clustering, then that is of course fine.

	Wolfgang


Michael Imbeault scripsit 08/03/10 18:53:
> Hello,
> 
> Is there a way to easily filter genes on the average signal over groups 
> (according to phenoData?). Let's say that in phenoData of my eset object 
> I have 'Time' and 'Status' variables, which have 3 values each. I have 3 
> arrays for each of the (9) conditions.
> 
> What I want is to keep genes with an average value of at least 100 in at 
> least one of the resulting 9 conditions. The genefilter package 
> seemingly only include functions to filter genes ignoring groups - is 
> there an easy way to do the same taking into account groups?
> 
> Thanks,
> Michael
> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact