[BioC] Separate Channel Analysis of Two-Color Data
smyth at wehi.EDU.AU
Wed Dec 13 03:36:40 CET 2006
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.
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.
>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?
>> > 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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