Affy PA calls
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Loren Engrav ★ 1.0k
@loren-engrav-2040
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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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Loren Engrav ★ 1.0k
@loren-engrav-2040
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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 >>>> >> >> >
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Mark Cowley ▴ 910
@mark-cowley-2951
Last seen 9.6 years ago
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
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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. >> >> _______________________________________________ >> 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 >
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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 > [[alternative HTML version deleted]]
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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 [[alternative HTML version deleted]]
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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
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hi Loren, the way i use P/M/A calls is to exclude probesets that are absent in all samples. This usually filters out 30-50% of the genes that are not expressed in your samples. Then let maanova/limma/SAM find the differentially expressed genes on those genes detected in at least one sample. If you really want to pursue your PA call idea, then you can calculate how many present calls there are in each group, and find genes that have 3 P's vs 0 P's in the 2 groups & vice versa: calls <- mas5calls( .... ) calls <- exprs(calls) Pcount.duroc <- apply(calls[,1:3] == "P", 1, sum) Pcount.york <- apply(calls[,4:6] == "P", 1, sum) HTH Mark On 30/07/2010, at 10:37 AM, Sean Davis wrote: > 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
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