[BioC] Extract M values from probes set to cluster

[Marcelo Laia]

Dear Sean

I thought that I did a mistake in selected. Then, I try... But no success.

Here are the outputs:

> selected  <- p.adjust(fit.2$p.value) <0.05
> summary(selected)
Mode   FALSE    TRUE    NA's
logical    2565     130     761
> length(selected)
[1] 3456
> MA.selected <- MA.2$M[selected, ]
> dim(MA.selected)
[1] 1782    3

I thought that I did a mistake here:

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

> selected  <- (fit.2$p.value) <0.05
> length(selected)
[1] 3456
> MA.selected <- MA.2$M[selected, ]
> dim(MA.selected)
[1] 4154    3
> fit.2 <- eBayes(fit)

Thank you very much

Laia

2007/2/13, Sean Davis <sdavis2 at mail.nih.gov>:
> 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)
>