[BioC] Creating a substet of probe intensities from AffyBatch object

Larry La Pointe larry.lapointe at csiro.au
Thu Sep 16 08:57:59 CEST 2004


Howdy,

I am trying to create a subset of probe intensities from an AffyBatch
object.  As a new user to the affy package (and Bioconductor, in
general) I was pleased to find an article presenting the package by
Gautier et al. in Bioinformatics (2004) 20:307-315.  I was *especially*
pleased to find the R code in Fig 4. which seems to do exactly what I'd
like:

## celdata is an AffyBatch of 75 arrays...
controls.gni<-grep("AFFX.+", geneNames(celdata))
controls.names<-geneNames(celdata)[controls.gni]
controls.indices<- indexProbes(celdata, which="pm", controls.names)

## so far so good....but:
controls.intensities<-intensity(celdata)[controls.indices, ]

gives:
Error: invalid subscript  ## ????

Am I missing something obvious?


BTW: Inspection of control.intensities show that this is a list object. 
By unlisting, such as:
x<-unlist(controls.indices)

I can recover the data but they are in a (rather nasty) vector.

thanks in advance,
LL


-- 
_____________________________________

Larry LaPointe

PhD Student
CSIRO / Flinders Univ / Enterix Inc.
Molecular Sciences/Bioinformatics
p (612) 9325 3250
m 04 0099 5027



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