[BioC] Gene names on topTable by limma

[James W. MacDonald]

Please don't take things off-list.

Marcos Pinho wrote:
> Jim,
>  
> thanks for your reply. I was already able to introduce gene symbols. 
> What I was looking for was to somehow create a column with short gene 
> names for my final report.

There isn't a getShortName() in annotate, but it isn't difficult to get 
these data directly:

names <- unlist(mget(fit$genes$ID, hgu133plus2GENENAME))

see ls("package:hgu133plus2.db") for all the annotation possibilities.

Best,

Jim


>  
> cheers,
>  
> Marcos
>  
> 
> *> library(limma)*
> 
> *> fit =lmFit (esetF, design)*
> 
> *> fit2=eBayes(fit)*
> 
> *> library(annotate)*
> 
> Loading required package: xtable
> 
>  
> 
> Attaching package: 'xtable'
> 
>  
> 
>  
> 
>         The following object(s) are masked from package:widgetTools :
> 
>  
> 
>          label
> 
>  
> 
> *> fit2$genes$Symbol=getSYMBOL(fit2$genes$ID, "hgu133plus2")*
> 
> *> topTable(fit2, coef=2)*
> 
> * *
> 
> *fit2$genes$EG <- getEG(fit2$genes$ID, "hgu133plus2")***
> 
>               ID Symbol     logFC  AveExpr         t      P.Value   
> adj.P.Val
> 
> 5253   209993_at  ABCB1  8.167898 6.410285  28.41936 1.387084e-06 
> 0.008649451
> 
> 3378  1553436_at  MUC19  7.512443 6.097913  25.70956 2.249499e-06 
> 0.008649451
> 
> 9828 206488_s_at   CD36  7.318355 6.081049  22.79634 4.015521e-06 
> 0.008649451
> 
> 6995 222392_x_at   PERP  6.047929 6.736659  20.28712 7.035669e-06 
> 0.008649451
> 
> 8973   210603_at  ARD1B  6.088776 5.773605  20.23547 7.122355e-06 
> 0.008649451
> 
> 1412   235683_at  SESN3  6.589716 5.620394  20.17661 7.222719e-06 
> 0.008649451
> 
> 7573 216191_s_at   TRD@ -6.153962 5.640399 -19.71517 8.071494e-06 
> 0.008649451
> 
> 4013   202948_at  IL1R1 -6.231328 5.580407 -19.61010 8.281240e-06 
> 0.008649451
> 
> 5302   205934_at  PLCL1  5.836512 5.809832  19.53496 8.435274e-06 
> 0.008649451
> 
> 4061 205786_s_at  ITGAM -6.788839 7.957034 -18.03301 1.238036e-05 
> 0.008649451
> 
> On Tue, Oct 6, 2009 at 4:18 PM, James W. MacDonald 
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> wrote:
> 
>     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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> 
> 
> 
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> 
>     -- 
>     James W. MacDonald, M.S.
>     Biostatistician
>     Douglas Lab
>     University of Michigan
>     Department of Human Genetics
>     5912 Buhl
>     1241 E. Catherine St.
>     Ann Arbor MI 48109-5618
>     734-615-7826
> 
> 
> 
> 
> -- 
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826