Affymetrix cytogenetics array

[Charles Mullighan]

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

[Cheng Li]

Charles,

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

Cheng

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[Shailender Nagpal]

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]

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

[Henrik Bengtsson]

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
single nucleotide polymorphism (SNP) content to identify loss of
heterozygosity (LOH), uniparental disomy (UPD), and regions
identical-by-descent. [...] The (i) Whole-Genome 2.7M Array [...]
provides 2.7 million markers, including 400,000 SNPs, to offer
superior resolution and enable detection of even the smallest
structural changes and regions of autozygosity. The (ii) Focused Array
includes more than 330,000 markers to enable efficient detection of
aberrations within focused regions of known cytogenetic importance. At
the same time, it maintains a backbone of markers at 16 kb spacing to
provide whole-genome coverage."

Cytogenetics_Array

> library("aroma.affymetrix");
> cdf <- AffymetrixCdfFile$byChipType("Cytogenetics_Array");
> print(cdf);
AffymetrixCdfFile:
Path: annotationData/chipTypes/Cytogenetics_Array
Filename: Cytogenetics_Array.CDF
Filesize: 538.32MB
Chip type: Cytogenetics_Array
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2015x2015
Number of cells: 4060225
Number of units: 2795708
Cells per unit: 1.45
Number of QC units: 4

There are 400,103 SNPs and 2,394,920 CN units in this CDF. 267,197
SNPs have only one probe pair, 104,264 SNPs have two probe pairs and
10,786 have three. There are also a small number of SNPs with more
probe pairs. 2,377,527 of the CN units are single CN probes (as in
GWS5 and GWS6). In addition to this, there are 1,775 CN units with
two probes, 5,618 with 3 probes, 1,496 with 7 probes, and 8,504 with 8
probes.

Affymetrix Product Page:
http://www.affymetrix.com/products_services/arrays/specific/cytogenetics_solution.affx
</qoute>

I think I found the CDF deep down inside the Chromosome Analysis Suite
(ChAS) Software zip file (same URL above).

/Henrik