Hi.
On Fri, Dec 7, 2012 at 5:21 AM, Hooiveld, Guido <guido.hooiv...@wur.nl> wrote:
> 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/
This great. To clarify, are you creating/releasing CDF *files*, or
only the various flavors of R packages containing that information?
I see that you are referring to 'PdInfo2Cdf.R'(*) on the site, which
indicates CDF files, but I cannot find such. (*) BTW, that script has
now been replaced by
http://aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo
Thanks,
Henrik
> 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
> 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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> You received this message because you are subscribed to the Google Groups
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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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>
> You received this message because you are subscribed to the Google Groups
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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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