[BioC] probability of a point membership to a certain cluster

[Steve Lianoglou]

Hi,

On Fri, Jan 27, 2012 at 8:28 AM, Barbara Uszczynska
<uszczynska at gmail.com> wrote:
> Dear Conductors,
>
> I was wondering if there's any simple way of calculating the probability of
> a point membership to a certain cluster. I'm using EM algorithm from mclust
> package to analyse my data. As an output of classification I obtain data
> grouped into clusters and I can have a matrix whose the element in position
> [I,k] presents the conditional probability of the ith point belongs to the
> kth cluster. However, I would like to get something more precise, as a
> probability of belongness for each point only from given cluster. For
> example, If I get my data divided into 3 groups by EM algorithm, I would
> like to know how strong each point from cluster 1 belongs to this cluster, how
> strong each point from cluster 2 belongs to this cluster and how strong
> each point from cluster 3 belongs to this cluster.

I probably shouldn't be answering these types of emails until I (at
least) finish my first coffee, but I'm a bit lost. The "thing" that
you are describing that you want is actually the `z` matrix you are
returned from Mclust (which you also describe above).

It's not clear (to me, anyways) how the second scenario you describe
is different than what z is -- hopefully someone else will be able to
ring in w/ more clarity.

> I was thinking about the
> creating some kind of parameter, which will allow me to see points with
> highest/strongest membership...like show me all points, which belong to
> their clusters with probability higher than 0.8.
>
> library(mclust)
>
> dataset1MC<-Mclust(dataset1)
> plot(dataset1MC, dataset1)
>
> dataset1MC$z

In your code above, you can just query `$z` for that, no? Wouldn't
this do what you want:

R> high.conf <- apply(dataset1MC$z, 1, function(row) any(row > 0.8))

Yes?
No?

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact