[BioC] Gene names on topTable by limma
James W. MacDonald
jmacdon at med.umich.edu
Tue Oct 6 22:56:19 CEST 2009
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
>
> [[alternative HTML version deleted]]
>
>
>
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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
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