[BioC] How to do clustering
sfalcon at fhcrc.org
Thu Jun 21 09:19:37 CEST 2007
"ssls sddd" <ssls.sddd at 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:
> 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 =
> 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:
> 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)
> Function: nsFilter (package genefilter)
> 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:
## choose the first item
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
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