[BioC] Limma, get the ranking position of a specific gene...

[Ramon Diaz-Uriarte]

Dear Emanuele,

Will this work?

(I take from the toptable help, modify the last call to toptable, to add a 
genelist, assign it it an object, and then use which; substitute the "100" in 
toptable by the number of genes you do have).

M <- matrix(rnorm(100*6,sd=0.3),100,6)
M[1,1:3] <- M[1,1:3] + 2
design <- cbind(First3Arrays=c(1,1,1,0,0,0),Last3Arrays=c(0,0,0,1,1,1))
fit <- lmFit(M, design=design)
fit <- eBayes(fit)
mytable <- topTable(fit, genelist = paste("gene", 1:100, sep = "."), 
number = 100)
which(mytable$ProbeID == "gene.8")



Best,

R.

On Friday 20 May 2005 19:36, E.Marchi wrote:
> Hi averybody,
> how can I get easily from an MarrayLM object the ranking position in the
> toptable of a gene? Suppose I only know  the ID... Apologies for the basic
> question.
> Regards.
>
> Emanuele
>
>
>
>  [[alternative HTML version deleted]]
>
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-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)




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