dChip Software Google Group

normalization

wlq...@gmail.com (Wendy Qiao) — Sat, 21 Nov 2009 16:17:21 UT

Dear Cheng,

I know you are very busy and I am sorry to bother you.

I am analyzing a set of HSC gene microarray. dChip crashes every time
when I try to normalize the data without giving error messages. I
wonder if the gene file and annotation file that I am using are not
compatible. From our collaborator, i.e., the owner of the CEL files,

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

mullig...@gmail.com (Charles Mullighan) — Tue, 17 Nov 2009 20:50:40 UT

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

Re: [dchip message 394] Affymetrix cytogenetics array

h...@stat.berkeley.edu (Henrik Bengtsson) — Tue, 17 Nov 2009 18:09:36 UT

Yes, here are my notes:

<qoute>
Cytogenetics_Array (Whole-Genome 2.7M Array; CYTO2)

From the Affymetrix press release 'New Cytogenetics Products Offer
Best Overall Approach for Detection of Chromosome Aberrations' (March
25, 2009): "The [two] Affymetrix Cytogenetics (i) Whole-Genome 2.7M
Array and (ii) Cytogenetics Focused Array include copy number (CN) and

RE: [dchip message 396] normalizing different array types together

lch3...@gmail.com (Cheng Li) — Tue, 17 Nov 2009 16:14:18 UT

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:

[link]

normalizing different array types together

shailendernag...@hotmail.com (Shailender Nagpal) — Tue, 17 Nov 2009 16:11:20 UT

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?

Problem Exporting Expression Values

leighton.st...@roswellpark.org (Stein) — Tue, 17 Nov 2009 15:57:15 UT

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-co ns.txt':try to put the
mapping file in the working directory'

RE: [dchip message 393] Affymetrix cytogenetics array

lch3...@gmail.com (Cheng Li) — Tue, 17 Nov 2009 15:52:51 UT

Charles,

We haven't modified dChip to handle this. Are there example CDF and
CEL files for the array type?

Cheng

-----Original Message-----
Sent: Monday, November 16, 2009 6:27 PM
To: dChip Software

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

Affymetrix cytogenetics array

mullig...@gmail.com (Charles Mullighan) — Mon, 16 Nov 2009 23:27:11 UT

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

Re: [dchip message 384] Re: snp6.0 call rate is 0

xuzho...@gmail.com (simon) — Mon, 02 Nov 2009 20:26:11 UT

Hi Cheng,
I use paired normal as reference and I choose median smoothing when I do
copy number analysis . However, I found big variation of copy number
intensity from some normal samples. They are not always close to 2, some
even higher than 4 or 5. Could you tell me some reasons?
Thanks
Simon

Affymetrix analysis call file not found

wlq...@gmail.com (Wendy Qiao) — Sun, 01 Nov 2009 23:52:43 UT

Dear all,

I am running a hematopoietic lineage microarray in dChip. The platform
is Addymetix HU133 Plus2.0. I download CSV file (HG-U133_Plus_2
Annotations, CSV format) from Affymetrix library and made a gene info
file using the gene info file (HG-U95Av2) on dChip webite as an
example. I wonder if I have to have all of columns in HG-U95Av2, as I

Re: [dchip message 388] Re: export PM/MM

wlq...@gmail.com (Wendy Qiao) — Sun, 01 Nov 2009 19:38:13 UT

Cheng,

I am sorry, I forgot to attached the CDF file.

Thanks,
Wendy

2009/11/1 Wendy Qiao <wlq...@gmail.com>

Re: [dchip message 388] Re: export PM/MM

wlq...@gmail.com (Wendy Qiao) — Sun, 01 Nov 2009 19:36:27 UT

Hi Cheng,

Thank you very much for your prompt reply. I tried "export expression value"
before. The file only has conditions in the first row, but no expression
levels are output. I guess it may because I did not give a gene information
file. I made a gene information file and run my microarray again. It gives

RE: [dchip message 387] export PM/MM

lch3...@gmail.com (Cheng Li) — Sun, 01 Nov 2009 18:50:00 UT

Wendy,

Use "Tools/Export expression value".

Cheng

-----Original Message-----
[mailto:dchip-software@googleg roups.com] On Behalf Of Wendy Qiao
Sent: Sunday, November 01, 2009 12:47 PM
To: dChip Software

Hi,

I am new to dChip. I would very appreciate if anyone can help me with
the following question:

export PM/MM

wlq...@gmail.com (Wendy Qiao) — Sun, 01 Nov 2009 17:47:10 UT

Hi,

I am new to dChip. I would very appreciate if anyone can help me with
the following question:

I am trying to export PM/MM. The output file that I got (using Tool--
"X","Y","Position","Probeset", "Probe", "Array","PM","MM","Bkgrd" and
"Theta". Is it possible to export a file with each column referring to

RE: [dchip message 385] Export probe Set ?

lch3...@gmail.com (Cheng Li) — Mon, 26 Oct 2009 02:43:50 UT

Arshi,

"Export probe set" will export probe level data, unnormalized or
normalized, that can be analyzed in other software such as R.

"Export expression" will export gene level expression values. For
E.coli it may output several thousand rows for all the probe sets.

Cheng

-----Original Message-----