[BioC] Gene names on topTable by limma

James W. MacDonald jmacdon at med.umich.edu
Tue Oct 6 21:18:09 CEST 2009

Hi Marcos,

Marcos Pinho wrote:
> Dear list,
> can anybody suggest how could I insert gene names in additional to gene
> symbols on my topTable generated by limma with my differentially expressed
> genes?

It really depends on what annotation you have for your genes. However 
the general idea would be to use one of the org.Xx.eg.db packages to 
annotate your genes, or if you are using a commercial chip, use a 
chip-specific annotation package.

Say your MArrayLM object is called 'fit'

tabl <- topTable(fit) ##maybe need a coef argument as well.

if you have Entrez Gene IDs

tabl$Genes <- unlist(mget(tabl$ID, org.Xx.eg.dbSYMBOL))

if you have an affy chip

tabl$Genes <- unlist(mget(tabl$ID, theaffychipSYMBOL))

or so.

Does that help?



> cheers,
> 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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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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