[BioC] Re: Bioconductor digest, Vol 1 #134 - 5 msgs
Larry
l.heisler@utoronto.ca
Thu, 17 Oct 2002 07:51:17 -0400
I have written R functions for MAS5.0 Signal and Background Correction
(Ideal MisMatch). I still need to test it out thoroughly though. If you
are interested I can send the code.
Regards
Larry Heisler
l.heisler@utoronto.ca
----- Original Message -----
From: <bioconductor-request@stat.math.ethz.ch>
To: <bioconductor@stat.math.ethz.ch>
Sent: Thursday, October 17, 2002 6:00 AM
Subject: Bioconductor digest, Vol 1 #134 - 5 msgs
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> Today's Topics:
>
> 1. Re: Obtain MAS5.0 Signal using affy (Isaac Neuhaus)
> 2. Re: Obtain MAS5.0 Signal using affy (Rafael A. Irizarry)
> 3. Re: Obtain MAS5.0 Signal using affy (Ben Bolstad)
> 4. Re: Obtain MAS5.0 Signal using affy (Kenny Ye)
> 5. Help with raw p-value (donghu@itsa.ucsf.edu)
>
> --__--__--
>
> Message: 1
> Date: Wed, 16 Oct 2002 09:27:09 -0400
> From: Isaac Neuhaus <isaac.neuhaus@bms.com>
> Subject: Re: [BioC] Obtain MAS5.0 Signal using affy
> To: Kenny Ye <kye@ams.sunysb.edu>
> Cc: bioconductor@stat.math.ethz.ch
>
> Kenny:
>
> A full description of the algorithm has been released by Affymetrix. I
have
> a perl version of MAS 5.0 and I will make it available as soon as
Affymetrix
> agrees to it.
>
> Regards,
>
> Isaac
>
> Ye wrote:
>
> > has anyone wrote a function for the MAS5.0 signal measure in affy? I am
> > processing DAT files of some customized chips, and couldn't find the CIF
> > file that MAS requires. As the CDF file is available, I am able to
process
> > DAT files and obtain CEL files using dChip, then import everything to
> > affy. Interesting how dChip does it without the CIF file but MAS insists
> > on it.
> >
> > I looked at Hubbell's powerpoint file on Terry's website, but the
> > equations given there are quite confusing. It shouldn't be difficult to
> > write the function as long as the formulae are set straight. following
is
> > my best guess
> >
> > Signal = Average of Tukey_Biweight(log(PM-CT))
> >
> > if MM < PM, CT=MM
> > if MM > PM, CT=PM/exp(proportion)
> >
> > proportion = Average of Tukey_Biweight(log(PM/MM)) (over all pairs
> > on the chip or just the set?). proportion is set to be 0 if the
> > average is negative.
> >
> > However, one still need to decide the support of the Tukey_Biweight
> > function. Maybe that doesn't matter much. Or simply take the
> > median. I don't understand why affymetrix doesn't want to disclose
> > their algorithm completely.
> >
> > Thanks in advance for your suggestions.
> >
> > Kenny
> >
> > Kenny Ye
> > Assistant Professor
> > Department of Applied Math and Statistics
> > SUNY at Stony Brook
> > Stony Brook, New York 11794-3600
> > Phone (631)632-9344
> > Fax (631)632-8490
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>
> --__--__--
>
> Message: 2
> Date: Wed, 16 Oct 2002 09:21:24 -0400 (EDT)
> From: "Rafael A. Irizarry" <ririzarr@jhsph.edu>
> Subject: Re: [BioC] Obtain MAS5.0 Signal using affy
> To: Kenny Ye <kye@ams.sunysb.edu>
> Cc: bioconductor@stat.math.ethz.ch
> Reply-to: rafa@jhu.edu
>
> we have plans to do this but not to high in the to-do list.
> obviously contributions are welcome.
>
> rafael
>
> On Wed, 16 Oct 2002, Kenny Ye wrote:
>
> >
> > has anyone wrote a function for the MAS5.0 signal measure in affy? I am
> > processing DAT files of some customized chips, and couldn't find the CIF
> > file that MAS requires. As the CDF file is available, I am able to
process
> > DAT files and obtain CEL files using dChip, then import everything to
> > affy. Interesting how dChip does it without the CIF file but MAS insists
> > on it.
> >
> > I looked at Hubbell's powerpoint file on Terry's website, but the
> > equations given there are quite confusing. It shouldn't be difficult to
> > write the function as long as the formulae are set straight. following
is
> > my best guess
> >
> > Signal = Average of Tukey_Biweight(log(PM-CT))
> >
> > if MM < PM, CT=MM
> > if MM > PM, CT=PM/exp(proportion)
> >
> > proportion = Average of Tukey_Biweight(log(PM/MM)) (over all pairs
> > on the chip or just the set?). proportion is set to be 0 if the
> > average is negative.
> >
> > However, one still need to decide the support of the Tukey_Biweight
> > function. Maybe that doesn't matter much. Or simply take the
> > median. I don't understand why affymetrix doesn't want to disclose
> > their algorithm completely.
> >
> > Thanks in advance for your suggestions.
> >
> > Kenny
> >
> >
> >
> >
> > Kenny Ye
> > Assistant Professor
> > Department of Applied Math and Statistics
> > SUNY at Stony Brook
> > Stony Brook, New York 11794-3600
> > Phone (631)632-9344
> > Fax (631)632-8490
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>
>
> --__--__--
>
> Message: 3
> Subject: Re: [BioC] Obtain MAS5.0 Signal using affy
> From: Ben Bolstad <bolstad@stat.berkeley.edu>
> To: Isaac Neuhaus <isaac.neuhaus@bms.com>
> Cc: Kenny Ye <kye@ams.sunysb.edu>, bioconductor@stat.math.ethz.ch
> Date: 16 Oct 2002 08:03:56 -0700
>
> You can find a full description of MAS5.0 (or at least the most complete
> I have seen) at
>
>
http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf
>
> Ben
>
>
> > Kenny:
> >
> > A full description of the algorithm has been released by Affymetrix. I
have
> > a perl version of MAS 5.0 and I will make it available as soon as
Affymetrix
> > agrees to it.
> >
> > Regards,
> >
> > Isaac
> >
> > Ye wrote:
> >
> > > has anyone wrote a function for the MAS5.0 signal measure in affy? I
am
> > > processing DAT files of some customized chips, and couldn't find the
CIF
> > > file that MAS requires. As the CDF file is available, I am able to
process
> > > DAT files and obtain CEL files using dChip, then import everything to
> > > affy. Interesting how dChip does it without the CIF file but MAS
insists
> > > on it.
> > >
> > > I looked at Hubbell's powerpoint file on Terry's website, but the
> > > equations given there are quite confusing. It shouldn't be difficult
to
> > > write the function as long as the formulae are set straight. following
is
> > > my best guess
> > >
> > > Signal = Average of Tukey_Biweight(log(PM-CT))
> > >
> > > if MM < PM, CT=MM
> > > if MM > PM, CT=PM/exp(proportion)
> > >
> > > proportion = Average of Tukey_Biweight(log(PM/MM)) (over all pairs
> > > on the chip or just the set?). proportion is set to be 0 if the
> > > average is negative.
> > >
> > > However, one still need to decide the support of the Tukey_Biweight
> > > function. Maybe that doesn't matter much. Or simply take the
> > > median. I don't understand why affymetrix doesn't want to disclose
> > > their algorithm completely.
> > >
> > > Thanks in advance for your suggestions.
> > >
> > > Kenny
> > >
> > > Kenny Ye
> > > Assistant Professor
> > > Department of Applied Math and Statistics
> > > SUNY at Stony Brook
> > > Stony Brook, New York 11794-3600
> > > Phone (631)632-9344
> > > Fax (631)632-8490
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>
>
> --__--__--
>
> Message: 4
> Date: Wed, 16 Oct 2002 13:17:49 -0400 (EDT)
> From: Kenny Ye <kye@ams.sunysb.edu>
> To: Ben Bolstad <bolstad@stat.berkeley.edu>, julien.sylvestre@wotan.ens.fr
> cc: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] Obtain MAS5.0 Signal using affy
>
>
> Ben and Julien, thanks for pointing me to this document. glad that they
> removed it from ``confidential''.
>
> Kenny
>
>
> Kenny Ye
> Assistant Professor
> Department of Applied Math and Statistics
> SUNY at Stony Brook
> Stony Brook, New York 11794-3600
> Phone (631)632-9344
> Fax (631)632-8490
>
> On 16 Oct 2002, Ben Bolstad wrote:
>
> > You can find a full description of MAS5.0 (or at least the most complete
> > I have seen) at
> >
> >
http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf
> >
> > Ben
> >
> >
> > > Kenny:
> > >
> > > A full description of the algorithm has been released by Affymetrix.
I have
> > > a perl version of MAS 5.0 and I will make it available as soon as
Affymetrix
> > > agrees to it.
> > >
> > > Regards,
> > >
> > > Isaac
> > >
> > > Ye wrote:
> > >
> > > > has anyone wrote a function for the MAS5.0 signal measure in affy? I
am
> > > > processing DAT files of some customized chips, and couldn't find the
CIF
> > > > file that MAS requires. As the CDF file is available, I am able to
process
> > > > DAT files and obtain CEL files using dChip, then import everything
to
> > > > affy. Interesting how dChip does it without the CIF file but MAS
insists
> > > > on it.
> > > >
> > > > I looked at Hubbell's powerpoint file on Terry's website, but the
> > > > equations given there are quite confusing. It shouldn't be difficult
to
> > > > write the function as long as the formulae are set straight.
following is
> > > > my best guess
> > > >
> > > > Signal = Average of Tukey_Biweight(log(PM-CT))
> > > >
> > > > if MM < PM, CT=MM
> > > > if MM > PM, CT=PM/exp(proportion)
> > > >
> > > > proportion = Average of Tukey_Biweight(log(PM/MM)) (over all pairs
> > > > on the chip or just the set?). proportion is set to be 0 if the
> > > > average is negative.
> > > >
> > > > However, one still need to decide the support of the Tukey_Biweight
> > > > function. Maybe that doesn't matter much. Or simply take the
> > > > median. I don't understand why affymetrix doesn't want to disclose
> > > > their algorithm completely.
> > > >
> > > > Thanks in advance for your suggestions.
> > > >
> > > > Kenny
> > > >
> > > > Kenny Ye
> > > > Assistant Professor
> > > > Department of Applied Math and Statistics
> > > > SUNY at Stony Brook
> > > > Stony Brook, New York 11794-3600
> > > > Phone (631)632-9344
> > > > Fax (631)632-8490
> > > >
> > > > _______________________________________________
> > > > Bioconductor mailing list
> > > > Bioconductor@stat.math.ethz.ch
> > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> >
> >
>
>
> --__--__--
>
> Message: 5
> To: bioconductor@stat.math.ethz.ch
> From: donghu@itsa.ucsf.edu
> Reply-To: donghu@itsa.ucsf.edu
> Date: Wed, 16 Oct 2002 15:54:56 PDT
> Subject: [BioC] Help with raw p-value
>
> I have played with multtest package using Golub data. After loading the
> dataset, I followed the steps descripted in the document to calculate t
> stat and raw p-values. Here are what I did:
>
> >teststat <- mt.teststat(golub, golub.cl)
> >rawp0 <- 2*(1-pnorm(abs(teststat)))
>
> Then I took a look of the t stat and raw p-value of the first gene. I
got:
>
> >teststat[1]
> [1] 1.759195
> >rawp0[1]
> [1] 0.07854436
>
> I also tried to calculate t stat and p-value of the first gene using
> t.test. I did the followings.
>
> > x <- golub[1,1:27]
> > y <- golub[1,28:38]
> > t.test(x,y)
>
> The result showed "t = -1.7592" and "p-value = 0.1062". I don't
> understand why the "p-value" I got here is different from "rawp0[1]"
> although the t stat is same. Can someone let me know why? Thank you in
> advance.
>
> Donglei Hu
> Gene Array Core Lab
> Diabetes Center
> UCSF
>
>
>
>
> --__--__--
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>
> End of Bioconductor Digest
>