Thanks Seth! I got a chance to check with nsFilter in genefilter package but
there is some problem with my dataset.

My codes are:

library(genefilter)

ans <- nsFilter(as.matrix(x), require.entrez = FALSE, require.symbol =
FALSE, require.GOBP = FALSE, require.GOCC = FALSE, require.GOMF = FALSE,
remove.dupEntrez = FALSE, var.func = IQR, var.cutoff = 0.75, var.filter =
TRUE)

ans$eset
ans$filter.log

and the error message is :

error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "nsFilter", for
signature "matrix"
>

And I did the following:

> library(genefilter)
> args(nsFilter)
function (eset, require.entrez = TRUE, require.symbol = TRUE,
    require.GOBP = FALSE, require.GOCC = FALSE, require.GOMF = FALSE,
    remove.dupEntrez = TRUE, var.func = IQR, var.cutoff = 0.5,
    var.filter = TRUE)
NULL
> showMethods("nsFilter")
Function: nsFilter (package genefilter)
eset="ExpressionSet"

Perhaps my matrix x is not compatible with "ExpressionSet"? Any suggestions
on this?

Thanks!

Sincerely,

Alex

On 6/20/07, Seth Falcon <sfalcon@fhcrc.org> wrote:
>
> Seth Falcon <sfalcon@fhcrc.org> writes:
>
> > "ssls sddd" <ssls.sddd@gmail.com> writes:
> >
> >> Thanks Martin. Converting my data frame to matrix soon solved
> >> the problem.
> >
> > Also, for non-specific filtering see the nsFilter function in the
> > Category package (latest release only) which provides an easy to use
> > interface for variance-based filtering.
>
> Sorry, nsFilter is actually in the genefilter package.
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
> Center
> http://bioconductor.org
>

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