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Puhong Gao
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140
@puhong-gao-116
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Hi, Dr. Dudoit,
Thank your group very much for the multtest package.
In reading your reply to Donglei's question, I am not sure how you got
=
the the df (11.049) for Golub data. Can you explain that? Thanks.
Regards,
Puhong Gao, PhD
Dept. of Developmental Psychobiology
NYSPI/Columbia University
1051 Riverside Drive
New York, NY 10032
(212) 543-3710
From: Sandrine Dudoit <sandrine@stat.berkeley.edu>
Date: Sat, 19 Oct 2002 20:46:03 -0700 (PDT)
To: <donghu@itsa.ucsf.edu>
Cc: Bioconductor mailing list <bioconductor@stat.math.ethz.ch>
Subject: Re: [BioC] Help with raw p-value
Hi,
The p-values in rawp0 are calculated based on a standard normal
distribution, while those in t.test are calculated based on a
t-distribution with df =3D 11.049.
Try
2*(1-pt(abs(teststat[1]),df=3D11.049))
and you will get the same p-value as with t.test.
Sandrine
----------------------------------------------------------------------
---=
---
---
Sandrine Dudoit, Ph.D. E-mail:
sandrine@stat.berkeley.edu
Assistant Professor Tel: (510) 643-1108
Division of Biostatistics Fax: (510) 643-5163
School of Public Health =
http://www.stat.berkeley.edu/~sandrine
University of California, Berkeley
140 Earl Warren Hall, #7360
Berkeley, CA 94720-7360
----------------------------------------------------------------------
---=
---
---
On Wed, 16 Oct 2002 donghu@itsa.ucsf.edu wrote:
> 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 =3D -1.7592" and "p-value =3D 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
>
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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<font face="3DArial" size="3D2">Hi, Dr. Dudoit,</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">Thank your group very much for the =
multtest=20
package.</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">In reading your reply to Donglei's =
question,=20
I am not sure how you got the the df (11.049) for Golub
=
data. Can=20
you explain that? Thanks.</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">Regards,</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2">Puhong Gao, PhD
Dept. of = Developmental=20 Psychobiology
NYSPI/Columbia University
1051 Riverside = Drive
New York,=20 NY 10032
(212) 543-3710
</font>
Dept. of = Developmental=20 Psychobiology
NYSPI/Columbia University
1051 Riverside = Drive
New York,=20 NY 10032
(212) 543-3710
</font>
<font face="3DArial" size="3D2"></font>
<font face="3DArial" size="3D2"><font face="3D"Times" new="" roman"="size=3D3">From: Sandrine=20
Dudoit <</font><font=20 face="3D"Times" new="" roman"="size=3D3">sandrine@stat.berkeley.edu</font><font=20 face="3D"Times" new="" roman"="" size="3D3">>
Date: Sat, 19 Oct 2002 = 20:46:03 -0700=20 (PDT)
To: <</font><font=20 face="3D"Times" new="" roman"="" size="3D3">donghu@itsa.ucsf.edu</font><font=20 face="3D"Times" new="" roman"="" size="3D3">>
Cc: Bioconductor mailing list=20 <</font><font=20 face="3D"Times" new="" roman"="size=3D3">bioconductor@stat.math.ethz.ch</font><font=20 face="3D"Times" new="" roman"="" size="3D3">>
Subject: Re: [BioC] Help with = raw=20 p-value
Hi,
The p-values in rawp0 are calculated based on = a=20 standard normal
distribution, while those in t.test are calculated = based on=20 a
t-distribution with df =3D=20 11.049.
Try
2*(1-pt(abs(teststat[1]),df=3D11.049))
and you = will get=20 the same p-value as with=20 t.test.
Sandrine
--------------------------------------- ---= ----------------------------------
---
Sandrine=20 Dudoit,=20 Ph.D. ;&n= bsp; =20 E-mail: </font><font=20 face="3D"Times" new="" roman"="size=3D3">sandrine@stat.berkeley.edu</font>
<font=20 face="3D"Times" new="" roman"="" size="3D3">Assistant=20 Professor & nbs= p; =20 Tel: (510) 643-1108
Division of=20 Biostatistics &nb sp;= =20 Fax: (510) 643-5163
School of Public=20 Health &nbs p;&= nbsp;=20 </font><font=20 face="3D"Times" new="" roman"="20" size="3D3">http://www.stat.berkeley.edu/~sandrine</font>
<font=20 face="3D"Times" new="" roman"="" size="3D3">University of California, = Berkeley
140 Earl=20 Warren Hall, #7360
Berkeley, CA=20 94720-7360
-------------------------------------------------------- ---= -----------------
---
On=20 Wed, 16 Oct 2002 </font><font=20 face="3D"Times" new="" roman"="" size="3D3">donghu@itsa.ucsf.edu</font><font=20 face="3D"Times" new="" roman"="" size="3D3"> wrote:
> I have played with = multtest=20 package using Golub data. After loading the
> dataset, I = followed=20 the steps descripted in the document to calculate t
> stat and raw = p-values. Here are what I did:
>
> >teststat <-=20 mt.teststat(golub, golub.cl)
> >rawp0 <-=20 2*(1-pnorm(abs(teststat)))
>
> Then I took a look of the t = stat and=20 raw p-value of the first gene. I got:
>
>=20 >teststat[1]
> [1] 1.759195
> >rawp0[1]
> [1]=20 0.07854436
>
> I also tried to calculate t stat and p-value = of the=20 first gene using
> t.test. I did the = followings.
>
>=20 > x <- golub[1,1:27]
> > y <- golub[1,28:38]
> = >=20 t.test(x,y)
>
> The result showed "t =3D -1.7592" and = "p-value =3D=20 0.1062". I don't
> understand why the "p-value" I got here = is=20 different from "rawp0[1]"
> although the t stat is same. Can = someone=20 let me know why? Thank you in
> advance.
>
> = Donglei=20 Hu
> Gene Array Core Lab
> Diabetes Center
>=20 UCSF
>
>
>=20 _______________________________________________
> Bioconductor = mailing=20 list
> </font><font=20 face="3D"Times" new="" roman"="size=3D3">Bioconductor@stat.math.ethz.ch</font>
<font=20 face="3D"Times" new="" roman"="" size="3D3">> </font><a=20 href="3D"http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor""><f ont="=20" face="3D"Times" new="" roman"="20" size="3D3">http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor</f>
<font=20 face="3D"Times" new="" roman"="20" size="3D3">>
_______________________________________________B= ioconductor=20 mailing list
</font><font=20 face="3D"Times" new="" roman"="size=3D3">Bioconductor@stat.math.ethz.ch</font>
<a=20 href="3D"http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor""><f ont="=20" face="3D"Times" new="" roman"="20" size="3D3">http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor</f>
</font></body></html>
------=_NextPart_000_001F_01C28F05.F5E7C1D0--
Date: Sat, 19 Oct 2002 = 20:46:03 -0700=20 (PDT)
To: <</font><font=20 face="3D"Times" new="" roman"="" size="3D3">donghu@itsa.ucsf.edu</font><font=20 face="3D"Times" new="" roman"="" size="3D3">>
Cc: Bioconductor mailing list=20 <</font><font=20 face="3D"Times" new="" roman"="size=3D3">bioconductor@stat.math.ethz.ch</font><font=20 face="3D"Times" new="" roman"="" size="3D3">>
Subject: Re: [BioC] Help with = raw=20 p-value
Hi,
The p-values in rawp0 are calculated based on = a=20 standard normal
distribution, while those in t.test are calculated = based on=20 a
t-distribution with df =3D=20 11.049.
Try
2*(1-pt(abs(teststat[1]),df=3D11.049))
and you = will get=20 the same p-value as with=20 t.test.
Sandrine
--------------------------------------- ---= ----------------------------------
---
Sandrine=20 Dudoit,=20 Ph.D. ;&n= bsp; =20 E-mail: </font><font=20 face="3D"Times" new="" roman"="size=3D3">sandrine@stat.berkeley.edu</font>
<font=20 face="3D"Times" new="" roman"="" size="3D3">Assistant=20 Professor & nbs= p; =20 Tel: (510) 643-1108
Division of=20 Biostatistics &nb sp;= =20 Fax: (510) 643-5163
School of Public=20 Health &nbs p;&= nbsp;=20 </font><font=20 face="3D"Times" new="" roman"="20" size="3D3">http://www.stat.berkeley.edu/~sandrine</font>
<font=20 face="3D"Times" new="" roman"="" size="3D3">University of California, = Berkeley
140 Earl=20 Warren Hall, #7360
Berkeley, CA=20 94720-7360
-------------------------------------------------------- ---= -----------------
---
On=20 Wed, 16 Oct 2002 </font><font=20 face="3D"Times" new="" roman"="" size="3D3">donghu@itsa.ucsf.edu</font><font=20 face="3D"Times" new="" roman"="" size="3D3"> wrote:
> I have played with = multtest=20 package using Golub data. After loading the
> dataset, I = followed=20 the steps descripted in the document to calculate t
> stat and raw = p-values. Here are what I did:
>
> >teststat <-=20 mt.teststat(golub, golub.cl)
> >rawp0 <-=20 2*(1-pnorm(abs(teststat)))
>
> Then I took a look of the t = stat and=20 raw p-value of the first gene. I got:
>
>=20 >teststat[1]
> [1] 1.759195
> >rawp0[1]
> [1]=20 0.07854436
>
> I also tried to calculate t stat and p-value = of the=20 first gene using
> t.test. I did the = followings.
>
>=20 > x <- golub[1,1:27]
> > y <- golub[1,28:38]
> = >=20 t.test(x,y)
>
> The result showed "t =3D -1.7592" and = "p-value =3D=20 0.1062". I don't
> understand why the "p-value" I got here = is=20 different from "rawp0[1]"
> although the t stat is same. Can = someone=20 let me know why? Thank you in
> advance.
>
> = Donglei=20 Hu
> Gene Array Core Lab
> Diabetes Center
>=20 UCSF
>
>
>=20 _______________________________________________
> Bioconductor = mailing=20 list
> </font><font=20 face="3D"Times" new="" roman"="size=3D3">Bioconductor@stat.math.ethz.ch</font>
<font=20 face="3D"Times" new="" roman"="" size="3D3">> </font><a=20 href="3D"http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor""><f ont="=20" face="3D"Times" new="" roman"="20" size="3D3">http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor</f>
<font=20 face="3D"Times" new="" roman"="20" size="3D3">>
_______________________________________________B= ioconductor=20 mailing list
</font><font=20 face="3D"Times" new="" roman"="size=3D3">Bioconductor@stat.math.ethz.ch</font>
<a=20 href="3D"http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor""><f ont="=20" face="3D"Times" new="" roman"="20" size="3D3">http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor</f>
