[BioC] Repeated gene entries on Toptable by limma

Chao-Jen Wong cwon2 at fhcrc.org
Fri Sep 11 21:05:14 CEST 2009

Hi, Marcos,

There are several ways you can do it. The easiest way is to to perform
some non-specific filtering using 'nsFilter' or 'featureFilter'
functions from the genefilter package. Assuming the probes set has
one-to-one mapping onto Entrez ID (there are some exception, but
rarely), you can remove probes that have duplicate Entrez ID by
     nsFilter(eset, remove.dupEntrez=TRUE, ...)
     featureFilter(eset, remove.dupEntrez=TRUE,...)

You can also manually pick the probe that has highest variation among
its duplicates before performing downstream analysis (limma).  Hope this
would help.


Marcos Pinho wrote:
> Dear list,
> I am a new user to the limma package for differential expression analysis
> and have recently noticed that when I generated my toptable with the 50 most
> differentially expressed genes that I have the same gene repeated more than
> once with diferent p values. Could someone suggest how to overcome this
> situation? Which values should I consider? Is there a way to condense this
> multiple entries into a single value for differential expression?
> Regards,
> Marcos B. Pinho
> Programa de Engenharia Química - PEQ
> Laboratório de Engenharia de Cultivos Celulares- LECC
> Universidade Federal do Rio de Janeiro - UFRJ
> Instituto Nacional de Câncer - INCA
> Rio de Janeiro - Brasil
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Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
cwon2 at fhcrc.org

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