[BioC] Affy PA calls

[Loren Engrav]

Sorry if was too terse

I have Affy chips from shallow and deep wounds in 3 Duroc and 3 Yorkshire
pigs. And I have the p-values from maanova and q-values from Storey q-values
which returned 171 probes of interest.

I would also like the 3 Durocs and the 3 Yorkshire bio reps to be the
"same".

So the general question is how to define "same"?

The specific question is can the Affy PA calls be used to define same?  If
one pig is PA meaning shallow is Present and deep is Absent, can I say the
other two pigs should also be PA?  Or is the PA call too suspect to be used
in this way?

Thank you





> From: Mark Cowley <m.cowley at garvan.org.au>
> Date: Fri, 30 Jul 2010 10:02:56 +1000
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Affy PA calls
> 
> hi Loren,
> please elaborate
> mark
> 
> On 30/07/2010, at 8:55 AM, Loren Engrav wrote:
> 
>> Does anyone put much stock in Affy PA calls?
>> 
>> I searched gmane and I think the answer is No. True?
>> 
>> Thank you.
>> 
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