Does anyone put much stock in Affy PA calls? I searched gmane and I think the answer is No. True? Thank you.

Ok, sounds as if p and q trump PA calls I will cease and desist on thinking to use PA calls after p and q to further refine things Thank you all > From: Mark Cowley <m.cowley at="" garvan.org.au=""> > Date: Fri, 30 Jul 2010 13:43:59 +1000 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Subject: Re: [BioC] Affy PA calls > > no worries. > i usually prioritise genes to follow up by small q-values and large logFC, but > if there's a low Pcount or a low average expression level, then that puts me > off too > > mark > On 30/07/2010, at 1:36 PM, Loren Engrav wrote: > >> Sorry, on the last email I hit your address rather than the BioC address >> >> >>> From: Loren Engrav <engrav at="" u.washington.edu=""> >>> Date: Thu, 29 Jul 2010 19:53:00 -0700 >>> To: Mark Cowley <m.cowley at="" garvan.org.au=""> >>> Conversation: [BioC] Affy PA calls >>> Subject: Re: [BioC] Affy PA calls >>> >>> Thank you >>> Ok, I will not cut further on the PA strings as described below >>> >>> But then as I look at the 171 probes of statistical interest without this PA >>> cut, I see a probe that is P on only one of 60 chips. >>> >>> In keeping with the "decision" that PA calls are too blunt to use to remove >>> probes, I suppose I should ignore that as well, again thinking that p and q >>> trump PA calls. True? >>> >>> >>> >>> >>> >>> >>>> From: Mark Cowley <m.cowley at="" garvan.org.au=""> >>>> Date: Fri, 30 Jul 2010 12:43:06 +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, >>>> 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. >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioconductor mailing list >>>>>>>>>> Bioconductor at 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 at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >> >> >

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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor