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Raw intensities for microarray data

Hello, I am preprocessing a microarray data and I want the raw intensities for all the samples. I used the function exprs() but the data frame had no probe annotation in the rownames. Can anyone help me to obtain the raw expression values with the probe IDs for the samples?

microarray geneexpression affymetrix r
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written by Vinesh • Vinesh

It's unclear where the problem is. Is this public data, and if so how did you obtain it and from where? What format do you have right now?

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written by ATpoint ATpoint

It is a publicly available data which I obtained from GEO platform. The format in which the files are right now is .CEL. I read the files and tried to obtain the expression of the files using exprs() function.

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written by Vinesh • Vinesh

1 answer

Install the "gcrma" package in R then

data.gcrma = gcrma(data)

exprs(data.gcrma)

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written by rishav513 • rishav513

gcrma normalizes the data and what I am looking for is just raw intensities corresponding to its probe IDs.

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written by Vinesh • Vinesh

Kindly show the step-by-step code that you followed and also the expression data info

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written by rishav513 • rishav513

setwd() library(affy) library(tibble)

celpath = "XXXXXX" #specify the CEL path

data = ReadAffy(celfile.path=celpath) #Import cel files

Obtain raw intensities

expr = exprs(data)

After this I obtain a matrix which has no probe IDs.

Expression data info Platform: Affymetrix Human Genome U133 Plus 2.0 Array (Obtained .CEL files from GEO)

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written by Vinesh • Vinesh

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