Question: ISO help making a heatmap from a subset of microarray probes in the expression set
0
gravatar for mat149
2.9 years ago by
mat14940
mat14940 wrote:

Hello,

 

I have a microarray expression set and I would like to select a subset of the RMA-normalized probeset intensities (rows) from the matrix and generate a heatmap using only the subset.  Can anyone deliver a script that will generate an R object containing only the probset ID's (rows) of my interest?

 

I can select one row with:

exprs(eset)[row#,1:16]

but I want the rows from all these probesetID's in one object: 12971238, 13099156, 13252591, 12970553, 13059863, 13240978, 13249882

 

This is my current script:

library(oligo)
CELlist <- list.celfiles("C:\\Users\\mat149\\Desktop\\GG\\CEL", full.names=TRUE, pattern=NULL, all.file=FALSE)
pdat<-read.AnnotatedDataFrame("C:\\Users\\mat149\\Desktop\\GG\\CEL\\phenoMOD.txt",header=TRUE,row.name="Filename",sep="\t")
CELdat <- read.celfiles(filenames = CELlist,experimentData=TRUE,phenoData=pdat,verbose=TRUE)
eset<-rma(CELdat, background=TRUE, normalize=TRUE, subset=NULL, target="core")     
library(affycoretools)
eset <- annotateEset(eset, annotation(eset))

 

 

thanks for looking into this,

Matt

oligo • 363 views
ADD COMMENTlink modified 2.9 years ago by James W. MacDonald51k • written 2.9 years ago by mat14940
Answer: ISO help making a heatmap from a subset of microarray probes in the expression s
0
gravatar for James W. MacDonald
2.9 years ago by
United States
James W. MacDonald51k wrote:

This is a very basic R question, and if you are getting tripped up by that, you should probably spend some time reading An Introduction to R.

Note that you can subset things using the [ function by passing a vector of numbers indicating which things you want (like you already did here: exprs(eset)[row#,1:16], using the vector 1:16), or by using a boolean vector of the same length as whatever you are subsetting that has TRUE for the positions you are interested in returning.

So how would one generate either the positions of those probeset IDs or a boolean vector? The canonical way is to use match, or the more intuitive %in% function. See ?match for more information.

ADD COMMENTlink written 2.9 years ago by James W. MacDonald51k
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