[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?
Best,
Jim
>
> 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.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
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