Here's the reply from Affymetrix Tech Support:
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Hello Dr Fass-
There is only a minor difference between the v1 and the v2 library
files and it has to do with the manufacturing controls on the array.
There is no difference with the probes interrogating the exons between
v1 and v2. Unfortunately, if you are trying to use our Expression
Console software, it will only recognize v2 library files so if you
have cel files that were scanned with v1 then we will need to convert
them to v2 in order to have the software recognize the files. Please
let me know if you need this work around and I am happy to send it to
you.
Casey
Casey Gates | AFFYMETRIX, INC. | Technical Support
3420 Central Expressway | Santa Clara, CA 95051
Tel:
888-362-2447 | Fax:
408-481-0435
sup...@affymetrix.com |
www.affymetrix.com
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I'll try taking the tack of that second announcement you found:
changing the chiptype in the CEL files ...
Thanks again,
~Joe
On Nov 26, 8:52 am, Joe Fass <
joseph.f...@gmail.com> wrote:
> Thanks Henrik and Mark,
>
> I had found the comment at the dChip forum that you found, Henrik, but
> wasn't convinced ... I'll try contacting Affymetrix and try doing some
> analysis, and post back here if that clears this up.
>
> ~Joe
>
> On Nov 25, 6:19 pm, "Henrik Bengtsson" <
h...@stat.berkeley.edu> wrote:
>
> > I found this comment by Cheng Li at the dChip forum: "You can rename
> > "HuEx-1_0-st-v2.pgf" to "HuEx-1_0-st-v1.pgf". I understand the two
> > should be for the same physical array, but just different annotation
> > of probes into probeset."
> > [
http://dchip.forum5.com/viewtopic.php?t=214&mforum=dchip]
>
> > More a long the same lines from Affymetrix: "changed the chiptype
> > setting in the CEL files fromHuEx-1_0-st-v1toHuEx-1_0-st-v2: This
> > >HuEx-1_0-st-v1CEL files. Did you get a very early version of these
> > > chips? From what I can tell from the Affymetrix web site, there is no
> > > annotation or anything available for this. But, typically the
> > > annotation from Affy is versioned separately. For example, from:
>
> > >
http://www.affymetrix.com/products_services/arrays/specific/exon.affx...
>
> > > you can see that the 'Annotations CSV' has version na21, na22, etc.
> > > This seems to be quite separate from thev1/v2notation.
>
> > > I know Ken had analyzed some data from an earlier version of the Exon
> > > chip, but that was not made commerically available.
>
> > > All this to say: I don't know. :)
>
> > > Cheers,
> > > Mark
>
> > > On 26/11/2008, at 12:22 PM, Henrik Bengtsson wrote:
>
> > >> I'll let the experts on exon arrays answer this, but for clarification
> > >> this question is related to page:
>
> > >>
http://groups.google.com/group/aroma-affymetrix/web/affymetrix-define...
>
> > >> /Henrik
>
> > >> On Tue, Nov 25, 2008 at 4:57 PM, Joe Fass <
joseph.f...@gmail.com>
> > >> wrote:
>
> > >>> This may not be the best place to ask this, but can I ask for a quick
> > >>> clarification about thev1/v2notation? Does this simply refer to