[BioC] more samr woes

[Holger Schwender]

Hi Iain,

no, the current version of siggenes does not contain functions for a quantitative analysis. However, you can write your own score function for performing such an analysis. An example on how such a function can be written is given in the siggenes vignette. Admittedly, this is a very easy example, and it will be more complicated to write a score function for the quantitative analysis -- in particular when you would like to estimate the expected d-values with a permutation based method, and do not want to assume a particular null distribution. But it is possible.

Good luck, ;-)
Holger 


-------- Original-Nachricht --------
> Datum: Wed, 7 May 2008 21:58:16 +0100 (BST)
> Von: IAIN GALLAGHER <iaingallagher at btopenworld.com>
> An: Sean Davis <sdavis2 at mail.nih.gov>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] more samr woes

> Thanks Sean - good advice.
> 
> I have used siggenes previously - great package, very easy to use. However
> I need to do quantitative analysis which I don't think siggenes does -
> feel free to enlighten me ;-)
> 
> cheers
> 
> iain
> 
> Sean Davis <sdavis2 at mail.nih.gov> wrote: On Wed, May 7, 2008 at 11:39 AM,
> IAIN GALLAGHER
>  wrote:
> > I've mostly solved my previous problem with samr (an issue with
> datatypes). However I now have the following problem. Whilst I can generate a
> sam.object and compute a delta table I cannot get samr to generate a list of
> significant genes.
> >
> >  The samr.compute.siggenes.table fails with:
> >
> >  Error in dimnames(res.up) = temp.names :
> >   length of 'dimnames' [2] not equal to array extent
> >
> >  This is after quantitative analysis.
> >
> >  Can anyone help with this?
> 
> Hi, Iain.  Your best bet is to write to the package maintainer (who
> may not be on this list since samr is not a bioconductor package).
> 
> As an alternative, have you considered the siggenes package for
> performing your sam analysis?
> 
> Sean
> 
> 
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> 
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