Dear James,
thanks for your help! I produced a plot exactly how I was imaging.

Priscila

On Tue, Aug 18, 2009 at 10:17 AM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> Hi Priscila,
>
> Priscila Grynberg wrote:
>
>> Dear BioCs,
>> I'd like to create a special volcano plot. Considering that I have genes
>> with high B values, and with low B values but with adj.P.Values
>> significantly. I'd like to highlight those with B and adj,P.values
>> positive
>> and those presenting only the adj.P.values positive.
>>
>> Is it possible to do that?
>>
>
> Of course! But you might have to do the plotting by hand rather than using
> a particular function.
>
> We can use the example for lmFit:
>
> sd <- 0.3*sqrt(4/rchisq(100,df=4))
> y <- matrix(rnorm(100*6,sd=sd),100,6)
> rownames(y) <- paste("Gene",1:100)
> y[1:2,4:6] <- y[1:2,4:6] + 2
> design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1))
> options(digit=3)
>
> # Ordinary fit
> fit <- lmFit(y,design)
> fit <- eBayes(fit)
>
> plot(fit$coef[,2], fit$lods[,2], pch = 16, cex = 0.35,
> xlab = "log Fold Change", ylab = "log Odds")
> bind <- fit$lods[,2] > 0
> points(fit$coef[bind,2], fit$lods[bind,2], pch = 16, cex = 0.5, col =
> "blue")
> pind <- p.adjust(fit$p.value[,2], "BH") < 0.05
> points(fit$coef[pind,2], fit$lods[pind,2], pch = 16, cex = 0.5, col =
> "red")
>
> These happen to color the same points, but from what you describe you will
> have both blue and red points.
>
> Best,
>
> Jim
>
>
>> Thanks for your help.
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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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
>



-- 
Priscila Grynberg, B.Sc., M.Sc.
Doutoranda em Bioinformática (Bioinformatics D.Sc student)
Laboratório de Genética Bioquímica
Universidade Federal de Minas Gerais
Tel: +55 31 3409-2628
CV: http://lattes.cnpq.br/8808643075395963

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