[BioC] CN analysis on a small Affymetrix GWS6 data set (Was: Re: QC Affy 6.0 SNP arrays with crlmm or Oligo?)

[Henrik Bengtsson]

Hi,

except from saying that genotyping is a much harder problem than CN
analysis, I'll only comment on the CN questions below.

On Wed, Mar 17, 2010 at 9:45 PM, jeremy wilson
<jeremy.wilson88 at gmail.com> wrote:
> Thanks for the reply dear Benilton..

[snip]

> In my case, how should I do the CNV analysis with only 8 samples. Are
> there any other packages or adjustments you can suggest me to
> compensate for the small sample size?

We also developed the CRMA copy-number methodology such that it is
possible to do the preprocessing on a single hybridization.  You still
need a reliable reference in order to calculate CN ratios.  You don't
say what your samples are, but if they are paired tumor-normals, you
can run CRMAv2 for the tumor and the matched normal and get
high-quality tumor-normal CN ratios (you won't get better results if
you have more arrays).  If you don't have paired data, you might be
able to use the robust average of the 8 samples as your reference -
again it may depend on what your samples are.  Using an external
reference (or pool of reference samples) is doable, but you will
definitely get better signal-to-noise ratios if you use an internal
(same lab) reference.

The CRMAv2 method is implemented in the aroma.affymetrix package:

  http://www.aroma-project.org/

(there you'll also find references to the method)

It is even possible to do LOH with small data sets, even better so in
paired tumor-normal settings, but we don't have a nice pipeline setup
for this yet.

/Henrik

>
> Please let me know
> Thank you
>
> On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho
> <beniltoncarvalho at gmail.com> wrote:
>> Hi Jeremy,

[snip]

>> About the sample size, you need at least 10 samples to use
>> crlmm::computeCopynumber.
>>
>> b
>>
>> On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson
>> <jeremy.wilson88 at gmail.com> wrote:
>>> Dear all,

[snip]

>>> One more question: I have only 8 arrays from the same lab and I need
>>> to do LOH and copy number analysis. Will the small number of arrays be
>>> problematic?
>>>
>>> Awaiting for your reply,
>>> Thank you
>>> JW
>>>
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>>
>
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