[BioC] Help with GSEA package

Martin Morgan mtmorgan at fhcrc.org
Fri Dec 3 07:19:03 CET 2010

Hi Jillian --

On 12/02/2010 06:27 AM, Jillian Rowe wrote:
> Hello all,
> I am very new to R, and am confused with the GSEA package.
> I am running an analysis on a group of CEL files from two treatment groups.

All that code was  bit intimidating!

> But I get this error:
> Error in as.list(getAnnMap("PATH2PROBE", annotation(idType))) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'as.list'

Unpack this a little. You're making a call to getAnnMap inside as.list.
What does getAnnMap return? I'd bet it throws an error

  getAnnMap("PATH2PROBE", annotation(idType))

and then unpack that and see how the argument


compares to the documentation ?getAnnMap. Perhaps you meant
annotation(gcrma_data_selected), but its hard to tell -- simplify the
code you present; in the process it might shed light on what the
underlying problem is.

Hope that helps!


> I have some sample data that uses data from the ALL library, and it inputs a
> data object from the genefilter function as well.
> Any help would be very, very appreciated.
> Thanks!
> Jillian
> 	[[alternative HTML version deleted]]
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