[BioC] AffylmGUI

[James W. MacDonald]

Chen, Kegui wrote:
> 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.

Technically, all three FDR methods are different. BH and BY are 
'one-step' methods that are based on the unadjusted p-value (which is 
computed using a t-distribution as the Null distribution), whereas SAM 
uses permutation to estimate the Null distribution and compute the so 
called q-value.

However, the interpretation of an FDR value is the same, regardless of 
how it is computed. Simply put, if you have a list of genes and the 
_largest_ FDR is 0.05, then you are estimating that 5% of the genes in 
that list are not really differentially expressed.

HTH,

Jim


> 
> 
> 
> 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.
> 
> 
> 
> Thanks!
> 
> 
> 
> 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 Gordon
> 
> 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
>>  Smyth 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,
>> 
>> Estrogen.
>> 
>>> Everything works for me but the FDR. I can not get FDR for the
>>> genes.
>> 
>> On
>> 
>>> 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
>> 
>> help
>> 
>>> 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 mean.
>> 
>> 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 Gordon
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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