Re: [dchip message 0] Digest for dchip-software - 5 messages in 2 topics

[Charles Mullighan]

Dear Cheng

The CDFs are in the ChAS (chromosome analysis suite) software download from Affy. There are also sample CELs from Affy, and we have our own. I can ftp these to you if you wish.

Charles

On Tue, Nov 17, 2009 at 12:07 PM, <dchip-s...@googlegroups.com> wrote:

 Today's Topic Summary

• Affymetrix cytogenetics array [4 updates]
• Problem Exporting Expression Values [1 update]

 Topic: Affymetrix cytogenetics array

Charles Mullighan <mull...@gmail.com> Nov 16 03:27PM -0800

 
Dear Cheng
Can/will dChip handle the new Affymetrix 2.7 million feature
cytogenetics array?
Charles Mullighan


 

"Cheng Li" <lch...@gmail.com> Nov 17 10:52AM -0500

 
Charles,
 
We haven't modified dChip to handle this. Are there example CDF and
CEL files for the array type?
 
Cheng
 
 
-----Original Message-----
From: Charles Mullighan [mailto:mull...@gmail.com]
Sent: Monday, November 16, 2009 6:27 PM
To: dChip Software
Subject: [dchip message 393] Affymetrix cytogenetics array
 
Dear Cheng
Can/will dChip handle the new Affymetrix 2.7 million feature
cytogenetics array?
Charles Mullighan
 
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"Shailender Nagpal" <shailend...@hotmail.com> Nov 17 11:11AM -0500

 
Hi Cheng,
 
How are you doing? I have a question for you...
 
I have two studies of HSC samples compared to GMP samples. One was done
using "Mouse 430 2.0" arrays, the other was done using "Mouse 430A 2.0"
arrays. I'd like to combine them and normalize the CEL files together.
 
Is there a way to do this with Dchip?
 
Are you aware of any approaches in literature for something like this?
 
Shailender Nagpal
 


 

"Cheng Li" <lch...@gmail.com> Nov 17 11:14AM -0500

 
Shailender,
 
430A contains a subset of probe sets in 430 2.0; so you can use 430A
probe set list (can be an exported file from "Tools/Export expression
value") as a common probe set file to export for both array types and
combine:
 
http://biosun1.harvard.edu/complab/dchip/combine%20chip.htm#combine_ar
ray
 
Cheng
 
 
-----Original Message-----
From: Shailender Nagpal [mailto:shailend...@hotmail.com]
Sent: Tuesday, November 17, 2009 11:11 AM
To: dchip-s...@googlegroups.com
Subject: [dchip message 396] normalizing different array types
together
 
Hi Cheng,
 
How are you doing? I have a question for you...
 
I have two studies of HSC samples compared to GMP samples. One was
done
using "Mouse 430 2.0" arrays, the other was done using "Mouse 430A
2.0"
arrays. I'd like to combine them and normalize the CEL files together.
 
Is there a way to do this with Dchip?
 
Are you aware of any approaches in literature for something like this?
 
Shailender Nagpal
 
--
This message is from the dChip Software user group.
-- If you ask dChip questions, please include dChip output messages,
generated files, or screenshots to help rapid debugging.
-- To post to this group, send email to
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at http://groups.google.com/group/dchip-software
 


 

 Topic: Problem Exporting Expression Values

Stein <leighto...@roswellpark.org> Nov 17 07:57AM -0800

 
Hi,
 
I am trying to export expression values for exon arrays using the hg-
u133 plus 2 mapping file found on the dchip website. However, when I
try to do so I get an error message saying 'Failed to read gene list
file 'C\New Folder\map.hg-u133-2.0-plus-cons.txt':try to put the
mapping file in the working directory'
 
The file is already in the the working directory. Can anyone help me
with this issue?
 
Thanks,
 
Leighton


 

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