Getting Probe Ids For Expression Matrix Before Summarisation (In R If Possible)
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10.9 years ago
Jimbo ▴ 120

Hi guys

Anyone know how to get the probe set ids for the expression matrix row names BEFORE summarisation (so like 140292811, 140292812 etc.). When I load the cel files into R, the original unnormalised expression matrix has row names from 1:number of probes:

library(oligo) 
geneCELs <- list.celfiles(path, full.names=TRUE)
affyGeneFS <- read.celfiles(geneCELs)
genePS <- rma(affyGeneFS, target="probeset") 
featureData(genePS) <- getNetAffx(genePS, "probeset")

so I can do exprs(genePS) and get the probesets, however I want the original probes, before they are "summarised" to the probe-set level. So something like: exprs(affyGeneFS). However this gives sequential row names as I said before.

Does anyone have any ideas? Perhaps the affy package is better suited?

J

r microarray • 3.7k views
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Entering edit mode
10.9 years ago
Christof Winter ★ 1.0k

Hi Jimbo,

If you have an Affymetrix chip which measures gene expression, I would indeed use the affy package instead of the oligo package. This should solve your problem with the missing probe set names.

Christof

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10.9 years ago
W Langdon ▴ 90

netaffy at affymetrix.com has descriptions of each of Affymetrix chip layouts which are compatible with bioconductor. You will need the one for the genechip you are using. Bill

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6.7 years ago
yywang113 ▴ 10

For some platforms, such as hugene 2.0 st, affy can not deal with the preprocessing part, only oligo or xps can deal with it.

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