Thank you both

Will try to explain better

Have Affy chips from shallow and deep wounds in 3 Duroc and 3 Yorkshire pigs

Prior to maanova and q-value I did strip all probes that were Absent on all
60 chips

Now then with maanova and q-value I have 171 probes of statistical interest,
but

In this set of 171 statistically selected probes, the detection string for a
given probe might be PAPAAP meaning

Shallow pig1 Present
Deep pig1 Absent

Shallow pig2 Present
Deep pig2 Absent

Shallow pig3 Absent
Deep pig3 Present

With these PA calls, pig3 is different.  I think I would like to remove this
probe from further consideration because even though it achieved p and q
significance, the pigs are not the same. Or are the PA calls so "blunt" that
they do not really indicate anything about shallow and deep, and after
stripping those absent on all 60 chips, are best ignored?

Thank you again both


From: Sean Davis <sdavis2@mail.nih.gov>
Date: Thu, 29 Jul 2010 20:37:25 -0400
To: Loren Engrav <engrav@u.washington.edu>
Cc: rbioc <bioconductor@stat.math.ethz.ch>
Subject: Re: [BioC] Affy PA calls



On Thu, Jul 29, 2010 at 8:28 PM, Loren Engrav <engrav@u.washington.edu>
wrote:
> 
> 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?
> 

That is a pretty blunt instrument.  

Doesn't your hypothesis test define sameness, at least relative to the other
group?  Again, you may need to elaborate a bit more on what you are doing.  

Sean

 
>> > From: Mark Cowley <m.cowley@garvan.org.au>
>> > Date: Fri, 30 Jul 2010 10:02:56 +1000
>> > To: Loren Engrav <engrav@u.washington.edu>
>> > Cc: rbioc <bioconductor@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.
>>> >>
>>> >> _______________________________________________
>>> >> Bioconductor mailing list
>>> >> Bioconductor@stat.math.ethz.ch
>>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> >> Search the archives:
>>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor




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