[BioC] Affy PA calls

Mark Cowley m.cowley at garvan.org.au
Fri Jul 30 04:43:06 CEST 2010


Hi Loren,
the mas5calls procedure generates Pvalues, and a call of Present just means P < threshold.
a PAP might mean 3 pvalues that are VERY similar to each other, and the 2nd is slightly higher than the threshold

a PAP also may mean that your gene is close to the limit of detection on the array, and that's always a dangerous place to be on a microarray.
I think the p/values from MAANOVA will be more robust than over-interpreting P/M/A calls, since it incorporates the within group measurement variance

cheers,
mark

On 30/07/2010, at 12:29 PM, Loren Engrav wrote:

> 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 at mail.nih.gov>
> Date: Thu, 29 Jul 2010 20:37:25 -0400
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Affy PA calls
> 
> 
> 
> On Thu, Jul 29, 2010 at 8:28 PM, Loren Engrav <engrav at 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 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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>>>> 
>> 
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> 
> 
> 
> 
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