Thanks Seth. I will read through it.

Sincerely,

Alex

On 6/21/07, Seth Falcon <sfalcon@fhcrc.org> wrote:
>
> "ssls sddd" <ssls.sddd@gmail.com> writes:
>
> > 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"
>
> Yes, nsFilter only supports ExpressionSet objects -- this is clearly
> stated in the man page for the function.
>
> > 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?
>
> A matrix object in R is certainly not equivalent to an ExpressionSet
> object.  I would recommend reading over the first vignette in the
> Biobase package: _An introduction to Biobase and ExpressionSets_.  You
> can get to it by doing:
>
>    library("Biobase")
>    openVignette(packge="Biobase")
>    ## choose the first item
>
> + seth
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
> Center
> http://bioconductor.org
>

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