View this page "Affymetrix transcript clusters definitions"

[epurdom]

Hello,
I wanted to let anyone who was interested know that new transcript
cluster cdfs for the Human Exon Array have been posted corresponding
to the NetAffx update of Nov. 12, 2007. I am now hosting these files
with collaborators at the Berkeley Cancer Genome Center (thanks Mark
for filling in). If you have any problems with the links, please
contact me directly.
Best,
Elizabeth
epu...@stat.berkeley.edu

Click on http://groups.google.com/group/aroma-affymetrix/web/affymetrix-defined-transcript-clusters
- or copy & paste it into your browser's address bar if that doesn't
work.

[Joe Fass]

This may not be the best place to ask this, but can I ask for a quick
clarification about the v1 / v2 notation? Does this simply refer to
more updated annotations? Is it valid to use the v2 cdf for v1 cel
files?

[Henrik Bengtsson]

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-defined-transcript-clusters

/Henrik

[Mark Robinson]

Hi Joe.

While I've analyzed several Exon array datasets, I have never seen any
HuEx-1_0-st-v1 CEL 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#1_4

you can see that the 'Annotations CSV' has version na21, na22, etc.
This seems to be quite separate from the v1/v2 notation.

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

------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.rob...@garvan.org.au
e: mrob...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------

[Henrik Bengtsson]

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 from HuEx-1_0-st-v1 to HuEx-1_0-st-v2: This
should mitigate chiptype mismatches when using 3rd party software with
the unsupported CDF file."
[http://www.affymetrix.com/analysis/netaffx/exon/announcements.affx]

Don't take it is a fact, but as a start. I'd say, send an email to
Affymetrix support (see their webpage) for a definite answer. If you
find out more about this, please let us know.

Also, at some stage there seems to have existed a 'HuEx-1_0-st-ta1'
chip type as well, cf.
http://www.affymetrix.com/support/developer/powertools/changelog/file-format-ps.html

Cheers

Henrik

[Joe Fass]

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 from HuEx-1_0-st-v1 to HuEx-1_0-st-v2: This
> should mitigate chiptype mismatches when using 3rd party software with
> the unsupported CDF file."
> [http://www.affymetrix.com/analysis/netaffx/exon/announcements.affx]
>
> Don't take it is a fact, but as a start.  I'd say, send an email to
> Affymetrix support (see their webpage) for a definite answer.  If you
> find out more about this, please let us know.
>
> Also, at some stage there seems to have existed a 'HuEx-1_0-st-ta1'

> chip type as well, cf.http://www.affymetrix.com/support/developer/powertools/changelog/file...
>
> Cheers
>
> Henrik

>
> On Tue, Nov 25, 2008 at 5:36 PM, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>
> > Hi Joe.
>
> > While I've analyzed several Exon array datasets, I have never seen any
> > HuEx-1_0-st-v1 CEL 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 the v1/v2 notation.
>
> > 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 the v1 / v2 notation?  Does this simply refer to
> >>> more updated annotations?  Is it valid to use the v2 cdf for v1 cel
> >>> files?
>
> > ------------------------------
> > Mark Robinson
> > Epigenetics Laboratory, Garvan
> > Bioinformatics Division, WEHI

> > e: m.robin...@garvan.org.au
> > e: mrobin...@wehi.edu.au

[Joe Fass]

Here's the reply from Affymetrix Tech Support:

*******************************************
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
*********************************************

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

> > should mitigate chiptype mismatches when using 3rd party software with
> > the unsupported CDF file."
> > [http://www.affymetrix.com/analysis/netaffx/exon/announcements.affx]
>
> > Don't take it is a fact, but as a start.  I'd say, send an email to
> > Affymetrix support (see their webpage) for a definite answer.  If you
> > find out more about this, please let us know.
>
> > Also, at some stage there seems to have existed a 'HuEx-1_0-st-ta1'
> > chip type as well, cf.http://www.affymetrix.com/support/developer/powertools/changelog/file...
>
> > Cheers
>
> > Henrik
>
> > On Tue, Nov 25, 2008 at 5:36 PM, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>
> > > Hi Joe.
>
> > > While I've analyzed several Exon array datasets, I have never seen any

> > >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

[Jun]

Hi,

I try to get help on finding annotation for the cluster id shown in
the cdf files.
For the human exon array, I saw the latest transcript cluster
annotation (.csv) dated as 11/24/08 at the Affymetrix website. The CDF
file I am using is from here and dated as Nov 2007 (core.R3). I
couldn't find either old transcript annotation or the newer cdf files.
Could anyboby give me a direction? Thanks.

[Mark Robinson]

Hi Jun.

Comments below.

You will notice that in the "Archived NetAffx Annotation Files"
section of:

http://www.affymetrix.com/products_services/arrays/specific/exon.affx#1_4

... you can find the older NetAffx files you need.

I did try and do an update last year sometime (July or so) and I
noticed that for the Human Exon array, none of the probesets had
changed in configuration, so I could've created a new CDF, but it
would be identical to the old one. Most of the changes in the NetAffx
CSV file were to do with other annotation, such as GO terms and so on.

When I get a free moment, I will have a look at the latest probeset
CSVs and see whether the probesets have in fact changed. If so, I'll
create a new CDF.

Either way, you should be ok by using a newer NetAffx annotation CSV
with the older CDF.

Hope that helps.

Cheers,
Mark

------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI

e: m.rob...@garvan.org.au
e: mrob...@wehi.edu.au

[telos]

Hi,

I'd like to run FIRMA on mouse Exon array data. For this, it seem that
I need special mouse Exon array CDF files... any advice on how I can
get hold of them?

Thanks

[Mark Robinson]

Hi.

Check the page for the MoEx-1_0-st chip, it has CDF files you can
download:
http://groups.google.com/group/aroma-affymetrix/web/moex-1-0-st

Cheers,
Mark