[BioC] Extract M values from probes set to cluster

[Marcelo Laia]

HI,

I would like to do a cluster in my topTable results.

I am start here:

selected  <- p.adjust(fit.2$p.value) <0.05

MA.selected <- MA.2$M[selected, ]

heatmap(MA.selected)
Error in hclustfun(distfun(x)) : NA/NaN/Inf in foreign function call (arg 11)

Then, I search in the archieves and found this function:

na.dist <- function(x,...) {
 t.dist <- dist(x,...)
 t.dist <- as.matrix(t.dist)
 t.limit <- 1.1*max(t.dist,na.rm=T)
 t.dist[is.na(t.dist)] <- t.limit
 t.dist <- as.dist(t.dist)
 return(t.dist)
}

x <- na.dist(MA.selected)
x <- as.matrix(x)
heatmap(x)

Work, but it cluster *all* probes on the data set!!! I would like to
cluster only 165 genes (p.value < 0.05)

How I need to do the heatmap with only toptable selected genes?

Could you help me, please.

Thank you


-- 
Marcelo Luiz de Laia
Ph.D Candidate
São Paulo State University (http://www.unesp.br/eng/)
School of Agricultural and Veterinary Sciences
Department of  Technology
Via de Acesso Prof. Paulo Donato Castellane s/n
14884-900   Jaboticabal - SP - Brazil
Phone: +55-016-3209-2675
Cell: +55-016-97098526