[BioC] Rif: Re: conditions to apply BH correction

[loredana.lepera at uniroma1.it]

   Dear Pavel,
   thanks a lot for your reply,
   but to be sure my question was clear enough,
   I would like if you gave a look at this link:
   [1]http://rss.acs.unt.edu/Rdoc/library/oneChannelGUI/html/rawpCheck.html
   What do you think about it?
   Loredana
   -----bioconductor-bounces at r-project.org ha scritto: -----

     Per: Loredana Le Pera [2]<loredanalepera at gmail.com>
     Da: Pavel Goldstein
     Inviato da: [3]bioconductor-bounces at r-project.org
     Data: 12/05/2011 06.16PM
     Cc: [4]bioconductor at r-project.org
     Oggetto: Re: [BioC] conditions to apply BH correction
     Hi Loredana ,
     1. Positive dependence is also Ok.
     2.  under the null hypothesis, the distribution of the p-values is
     Uniform[0,1] - it can be proved.
     So this is assumption of the method, you do not have to check it.
     Pavel
     On Thu, May 12, 2011 at 5:11 PM, Loredana Le Pera
     [5]<loredanalepera at gmail.com>wrote:
     > Dear List,
     >
     > I would like to understand if/when Benjamini-Hochberg correction can be
     > applied and if not, what kind of correction is possible to apply.
     >
     > From the oneChannelGUI package vignette:
     >
     > "The function raw p-value distribution is implemented to evaluate if the
     BH
     > type I error correction methods could be used. To apply BH correction
     two
     > conditions should be satisfied:
     > 1. The gene expressions are independent from each other.
     > 2. The raw distribution of p-values should be uniform in the non
     > significant range."
     >
     >
     > My doubts mainly concern the second condition:
     >  - what does it mean exactly?
     >  - where does it come from?
     >
     > If this condition is not true, what  I can do to consider multiple
     testing
     > correction?
     >
     >
     > Thanks for any reply or suggestion,
     > Loredana.
     >
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References

   1. http://rss.acs.unt.edu/Rdoc/library/oneChannelGUI/html/rawpCheck.html
   2. mailto:loredanalepera at gmail.com
   3. mailto:bioconductor-bounces at r-project.org
   4. mailto:bioconductor at r-project.org
   5. mailto:loredanalepera at gmail.com
   6. mailto:Bioconductor at r-project.org
   7. https://stat.ethz.ch/mailman/listinfo/bioconductor
   8. http://news.gmane.org/gmane.science.biology.informatics.conductor
   9. mailto:Bioconductor at r-project.org
  10. https://stat.ethz.ch/mailman/listinfo/bioconductor
  11. http://news.gmane.org/gmane.science.biology.informatics.conductor