[BioC] Separate Channel Analysis of Two-Color Data

[Gordon Smyth]

That's right. The avedups() function in fact assumes the same number 
of replicates (as for the duplicateCorrelation function).

The situation is clouded slightly by missing values,so I recommend 
that Weiyin pre-process to avoid them.

Cheers
Gordon

At 12:55 PM 13/12/2006, Naomi Altman wrote:
>You have to be a bit careful here.  Averaging works if all the genes 
>have the same number of replicates.  If not, then averaging will 
>violate the variance assumptions, although you might be able to 
>mitigate this by using spot weights.  On spotted arrays, one usually 
>does have the same number of replicates, but on Agilent arrays, it 
>is up to the array designer.
>
>--Naomi
>
>At 04:58 PM 12/12/2006, Gordon K Smyth wrote:
>>On Wed, December 13, 2006 5:16 am, Weiyin Zhou wrote:
>> > Dr. Smyth and limma users,
>> >
>> > If I want to do separate channel analysis of two-color Agilent data
>> > file, how can I deal with replicated spots within array?
>> >
>> > According to limma User's Guide, Chapter 9, for doing separate channel
>> > analysis of two-color data, the correlation to be estimated is that
>> > between the two channels for the same spot rather than between
>> > replicated spots.   So how can I get one value for the replicated spots
>> > within array?  In ratio base, it gets one p value for the replicated
>> > spots by use function duplicateCorrelation and ndups=2.
>> >
>> > I am thinking maybe I should do average of replicated spots within array
>> > first, then do intraspotCorrelation to get estimate the correlation.
>>
>>That's what I would do.
>>
>> > But I don't know what kind of function available for doing it?
>>
>>?avedups
>>
>>Best wishes
>>Gordon
>>
>> >
>> >
>> >
>> > Could you help me?
>> > Thanks in advance,
>> >
>> > Regards,
>> >
>> > Weiyin Zhou
>> > Statistics and Data Analyst
>> > ExonHit Therapeutics, Inc.
>> > 217 Perry Parkway, Building # 5
>> > Gaithersburg, MD 20877
>> >
>> > email: Weiyin.zhou at exonhit-usa.com <mailto:Weiyin.zhou at exonhit-usa.com>
>> > phone: 240.404.0184
>> > fax: 240.683.7060
>>
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>
>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
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>