Hi, I am trying to analyze a microarray dataset with platform “[HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [HuGene20stv1_Hs_ENTREZG_17.0.0]”. I have read almost all papers which published datsets using this platform in last 4 years. In all of these affy package was used to read cel files. But when I try to do that then R produces the error “The affy package is not designed for this array type. Please use either the oligo or xps package.” which is not reported in literature previously. Additionally when I use oligo package then cel files are read but probeset ids are not right. can someone please help me with this.
my script when I use affy package
library(affy)
data <- ReadAffy()
and this results in warning
Error:
The affy package is not designed for this array type.
Please use either the oligo or xps package.
So I tried using Oligo package using script as below after setting up the directory where cel files are :
library(oligo)
library(limma)
library(hugene20sttranscriptcluster.db)
library(annotate)
library(dplyr)
celFiles = list.celfiles()
rawData = read.celfiles(celFiles)
probesetData = rma(rawData)
probeset.expression = exprs(probesetData)
head(probeset.expression[,c(1,2,3)])
but the problem is all the probesets here are wrong.
16650001
16650003
16650005
16650007
16650009
16650011
these should be something like
100009613_at
100009676_at
10000_at
10001_at
10002_at
100033413_at
100033422_at
100033423_at
100033424_at
