dChip Software Google Group

normalization

2009-11-21T16:17:21Z

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

2009-11-17T20:50:40Z

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

2009-11-17T18:09:36Z

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

2009-11-17T16:14:18Z

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

2009-11-17T16:11:20Z

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

2009-11-17T15:57:15Z

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

2009-11-17T15:52:51Z

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

2009-11-16T23:27:11Z

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

2009-11-02T20:26:11Z

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

2009-11-01T23:52:43Z

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

2009-11-01T19:38:13Z

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

2009-11-01T19:36:27Z

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

2009-11-01T18:50:00Z

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

2009-11-01T17:47:10Z

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 ?

2009-10-26T02:43:50Z

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-----