[BioC] Extract M values from probes set to cluster

[Sean Davis]

On Tuesday 13 February 2007 06:12, Marcelo Laia wrote:
> 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)

What is the output of:

length(selected)

and 

dim(MA.selected)