ExpressionSet subsetting

Question

I have an ExpressionSet object that I want to subset. For example,

> str(ESet)
Formal class 'ExpressionSet' [package "Biobase"] ..
  ..@ assayData        :..         
  ..@ phenoData        :
  .. .. .. ..$ STATUS  : num [1:210] 1 1 1 1 1 1 1 1 1 1 ...
  ....

I want to extract a subset where STATUS==0. I've tried:

exprs(ESet@phenoData$STATUS==0)

but it does not work.

Abomb

Answer 1

You are almost there. Guessing at your data structure, I think the following should work:

exprs(ESet)[ESet@phenoData$STATUS==0,]

If you look at this paper, there are lots of examples of sub-setting the data depending on strain and time. I should admit that I'm an author on this paper.

Arica

@Joris: I'm always a bit embarrassed about self promotion - I'm British after all - but when I analysed my first microarray data set, I wish I had a similar paper to look at. – Arica

Use ESet$STATUS == 0; see the Biobase landing page and "An Introduction to Biobase and ExpressionSet" section "ExpressionSet basics", in addition to ?ExpressionSet. – Diaster

@Arica : Could you please update the link, the old one seems to be dead – Jemappes