Dear Kasper,

Thank you very much for your suggestion.
I'll try to play around with the oligo package.
However, I'm not an expert so I'll not be able to go very deep on the
internal structures.

Alternatively, I can normalize my data before (in a different software like
Dchip) and  them use the limma package for the analysis of gene expression.

Best regards,
Helga


On Mon, May 9, 2011 at 4:48 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Helga,
>
> others may contribute with their perspectives, but the main problem is
> that you have a very atypical affymetrix setup by not having MM probes
> at all.  The concept of a CDF package is really build around having MM
> probes.  Now, an expert user (me for example) can work around this by
> knowing the internal structures well, but this is not something that
> works out of the box.
>
> You could try looking into the oligo package that supports the newer
> Gene chips (that also have no MM probes as far as I recall, but does
> have background probes), I don't know how easy it will be to make a
> ProbeDesign package for your custom setup.  Regular users of Oligo
> might have some perspective here.
>
> This will probably be a problem no matter what analysis suite you are
> using (Bioconductor or something else).
>
> Kasper
>
> On Mon, May 9, 2011 at 4:18 AM, Helga Garcia <hmcfgarcia@gmail.com> wrote:
> > Dear all,
> >
> > We have developed our own Affymetrix chip (Custom Express Array, PM-only
> > with two species).
> > I want to analyse the data with the limma package, but for that I need to
> > built my own CDF package,
> > probe package and built the filters to analyse one specie or another.
> > I'm using the makeProbePackage available in the AnnotationDbi (for a
> > R-2.13.0) but I got the following error message:
> >
> > Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument
> >
> > I already tried an old version of R-2.9.1 with a package matchprobes
> (that
> > is no longer update for R-2.13.0)
> > but the same error occurs.
> >
> > Does anyone knows how could I overcome this problem?
> > Thank you very much for your attention.
> > Best Regards,
> > Helga
> >
> >
> >
> > --
> > Helga Garcia
> >
> > PhD student
> > Applied and Environmental Mycology Lab/Molecular Thermodynamics Lab
> >
> > ITQB I - UNL
> > Portugal
> >
> >        [[alternative HTML version deleted]]
> >
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> >
>



-- 
Helga Garcia

PhD student
Applied and Environmental Mycology Lab/Molecular Thermodynamics Lab

ITQB I - UNL
Portugal

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