[BioC] decideTests with nestedF

Pedro López Romero plopez at cnic.es
Fri Jun 16 15:55:28 CEST 2006

Hi Jim, thank you so much for the replay.- 

I am not using decideTests ( ) to filter the genes. I am using p.adjust ()

ord=which(p.adjust(fit2$F.p.value,method="fdr") < 0.05)

Then, I use the list of genes that result to be significant to apply 
decideTests (..., method="separate"). I thought that this could be
conceptually similar as using decideTests (..., method="nestedF"). 

I understand that "nestedF" follows a step-wise procedure selecting first
genes using their moderated F-statistic, and second (for the selected gene)
selecting the contrast that contributes to the significance of the F by the
largest value of their moderated t-statistics. I think that this is clear to
me. As a matter of fact you explained this recently:  

So now, instead of using "nestedF", why is not possible to select genes in a
two-step-wise procedure?, firstly using a F-test to select genes that are
differentially expressed in at least one contrast and from this list of
selected-genes, to select the genes that are significant contrast by
contrast. It would be similar to nestedF, but instead of selecting the
contrast by the largest t-statistic, I perform a t-statistic for the whole
set of "selected-F-genes" for every contrast. 

On the other hand, when using "nestedF" I get some genes with a 0.9 adjusted
p-value, that probably should not be considered as diferentially expressed. 

>To answer your original question, I think the problem arises in this 
>line of your code:

> decideTests(fit2,method="nestedF",adjust.method=”fdr”,p.value=0,05)

Yes, this I re-typed the code wrongly. In my R-script is 0.05  

Again, thanks for your time.- 


-----Mensaje original-----
De: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] En nombre de James W.
Enviado el: viernes, 16 de junio de 2006 15:01
CC: 'Bioconductor'
Asunto: Re: [BioC] decideTests with nestedF

Hi Pedro,

Pedro López Romero wrote:
> Hi Sean, 
> thanks a lot for the replay. 
> Yes, you understood my doubt. I have several experimental conditions, and
> thought that filtering first by the moderated F-statistic would be a right
> approach, since by this I would be selecting the genes that are DE in any
> the contrasts. Now, from this reduced list, I thought that I could select
> the genes for every independent contrast given by my experimental
> conditions. 

I don't think you understand what decideTests() is doing. This function 
fits all the contrasts in your contrasts matrix, using one of several 
different methods. So you cannot use decideTests() to filter your genes 
before doing the contrasts, because decideTests() _is_ doing the contrasts.

As Sean mentioned, if you want to pre-filter your genes, you should be 
filtering using an agnostic approach such as removing those genes that 
have a low variance across all samples.

To answer your original question, I think the problem arises in this 
line of your code:


If this is a direct copy-paste of your code (and not a re-typing), then 
you made a mistake in your p.value argument. It should read 0.05, not 0,05.



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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