[BioC] Textual description of affy

[Ben Bolstad]

That looks like an error in the vignette which will be corrected.
Usually with expresso() you need to specify a method for each of the
four steps. In this case it looks like the example forgot to include the
pmcorrect.method. You should find something like

eset<-expresso(Data,normalize.method="qspline",bgcorrect.method="rma",pmcorrect.method="pmonly",summary.method="liwong")

should work fine.

Thanks,

Ben




On Tue, 2003-06-24 at 06:29, Michael Barnes wrote:
> I am trying to work through the Vignette entitled "textual description
> of affy" and am encountering errors.  Everything is fine until I reach
> page 10, the first command, at which point I received several erros that
> I have worked through to give me the following command:
> 
> >
> eset<-expresso(Data,normalize.method="qspline",bgcorrect.method="rma",summary.method="liwong")
> 
> I am now getting the following error and am unsure how to fix this:
> 
> Error in expresso(Data, normalize.method = "qspline", bgcorrect.method
> = "rma",  : 
>         pmcorrect.method missing
> 
> If I was not supposed to "correct" the command this way, how should I
> have worked through the errors ("unused argument(s) (bg.method ...)?"
> and " Object "affybatch" not found"). I have used "Update packages from
> Bioconductor" and "Update packages from CRAN" to no avail.
> 
> Any help would be appreciated.
> 
> Michael Barnes
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad