[BioC] AffylmGUI

Chen, Kegui chenkeg at missouri.edu
Fri Apr 14 04:56:49 CEST 2006

Hi, All:


   Following the answer from Gordon, I have another question about the FDR.   Since there two adjust method fro FDR in R.2.2.0, BH and BY, which one is the FDR used in SAM? The FDR in SAM is different from any above BH or BY?  From SMA   there is a FDR number (for example 5%) with the identified differential gene list. From the AffylmGUI there is adjusted P value (FDR) with every gene. 


   I think that the FDR 5% in SAM means that there are 50 false discovery genes in a of list 10000 genes. So, is there any possibility to know the number of false discovery genes in the differential gene list (for instance 1000 genes) by BH or BY adjusted P value from AffylmGUI. For me,  the FDR idea of SMA is more clearly stated to make me comfortable.


  I am not a statistician.  Probably my questions do not make sense in statistics. However, I think it makes sense to biologist.




 K. Chen


From: Gordon Smyth [mailto:smyth at wehi.edu.au]
Sent: Thu 4/13/2006 12:25 AM
To: Chen, Kegui
Cc: BioC Mailing List; Keith Satterley
Subject: RE: [BioC] AffylmGUI

Dear K Chen,

The new option "BH" is the same as the old option "fdr". The new
names were introduced into the p.adjust() function in R 2.2.0 because
there are now two FDR control methods (BH and BY). See ?p.adjust

We removed the Bonferroni, Hochberg and Hommel options because we
don't think these are ever the best options for microaray data.

Best wishes

At 01:33 PM 13/04/2006, Chen, Kegui wrote:
>Dear Gordon:
>   I am very sorry for the confusion.
>   The R program I used is Version 2.2.1. The AffylmGUI I used is Version
>1.5.4. Limma is Version 2.4.12. The data I used is the example data,
>Estrogen. My computer is windows PC.
>   I followed the instruction provided in the program step by step. When
>open the Toptable What I can see in the Toptable options is not the one
>provided in the instruction. The difference is in the Adjust method. In
>the instruction there the following options: Bonferroni, Holm, Hochberg,
>Hommel, FDR and None, total 6 options. What I see in my computer is
>None, BH, BY, Holm, total 4 options. I' like to know FDR since it is
>popular now.
>   Please explain it.
>   Thanks!
>   K. Chen
>-----Original Message-----
>From: bioconductor-bounces at stat.math.ethz.ch
>[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon
>Sent: Wednesday, April 12, 2006 12:25 AM
>To: Chen at wehi.edu.au; Kegui at wehi.edu.au.chenkeg.at.missouri.edu
>Cc: BioC Mailing List
>Subject: [BioC] AffylmGUI
> >[BioC] AffylmGUI
> >Chen, Kegui chenkeg at missouri.edu
> >Wed Apr 12 04:30:28 CEST 2006
> >
> >Hi, Dear all:
> >
> >     I am new here. I run the AffylmGUI using the example data,
> >Everything works for me but the FDR. I can not get FDR for the genes.
> >the manual, it looks that there are 6 choices for the adjust method.
> >However, I can not get 5 choices without FDR in my computer? Please
> >me to solve this issue.
> >
> >   Thanks!
> >   K. Chen
>Dear K Chen,
>When you ask for help, you need to give other people on the list
>enough information to be able to help you. It doesn't tell us
>anything to say that you can't get something. We're not looking over
>your shoulder while you work at your computer and we can't see what you
>You need to tell us in detail
>i) what you did, and
>ii) what output you got from the software
>iii) why you think what you got is not correct
>Remember, you need to tell us the facts as in (i) and (ii), not an
>interpretation of them.
>You also need to tell us exactly what version of R and affylmGUI you
>are using, and on what sort of computer.
>Best wishes

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