Hi,
To follow up on Henrik's suggestion: we recently have made
Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as well,
essentially using the PD.Info packages. Please find them here:
http://nmg-r.bioinformatics.nl/
HTH,
Guido
-----Original Message-----
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Thursday, December 06, 2012 21:45
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays
On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka <maria.tr...@ifr.ac.uk> wrote:
> Hi guys,
> probably you've already given the answer somewhere but can i use
> aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)?
> Presumably the same way as 1.0 arrays?
I'm not working with those myself, and I don't know the exact design details on
those chips, but, yes, most likely the same way as the previous ST arrays.
What is not available out of the box is a CDF file for these 2.0 ST arrays
(i.e. HuGene-2_0-st-v1 and ). Unless you find such CDFs from the various
groups providing custom CDFs, you need to create them yourselves. Here you've
got a few options, but I would try with what's explained in how-to page 'Create
a CDF file from Bioconductor Platform Design (PD) Info package', which you find
via http://aroma-project.org/howtos/
/Henrik
>
> Thanks in advance,
> Maria
>
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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