[BioC] Filter over group averages
whuber at embl.de
Thu Mar 11 16:17:32 CET 2010
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.
Michael Imbeault scripsit 08/03/10 18:53:
> 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?
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