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Illumina bead chip data normalisation

Hi guys, could you suggest me a way to normalize Illumina expression beadchip data?

For example, starting from the GSE32025_non-normalized.txt.gz file, could you suggest me some few steps (preferentially in R) to finally obtain a normalized data matrix as for Affymetrix RMA normalisation? I suppose this is an intensity "count" matrix. When I started reading it using limma and the following instruction: idata <- read.ilmn("GSE32025_non-normalized.txt",probeid = "ID_REF",expr="SKBR"), the following error appeared: 

Error in readGenericHeader(fname, columns = expr, sep = sep) : 
  Specified column headings not found in file
In addition: Warning message:
In grep(a, txt) : input string 1 is invalid in this locale

I don't know how to deal with this error since this is the first time for me that I analyse this kind of data.

Can anyone help me please?

Thank you in advance

e.

illumina gene expression limma
• 3,479 views • link
updated by murshad.60ali • murshad.60ali • written by elb elb

Hi elb,

please do not double-post your question. I deleted the duplicate. This is a question, not a job offer. Please use the code formatting option code to indicate code and error messages for matters of readability. I have done it for you this time.

• 1 views • link
written by ATpoint ATpoint

thank you ATpoint and sorry.

• 1 views • link
written by elb elb

Thank you very much Kevin!

useful for text file also

• 0 views • link
written by murshad.60ali • murshad.60ali

1 answer

You can download the already-normalised data with:

library(Biobase)
library(GEOquery)

# load series and platform data from GEO
gset <- getGEO("GSE32025", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL6885", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

dev.new(width=4+dim(gset)[[2]]/5, height=6)
par(mar=c(2+round(max(nchar(sampleNames(gset)))/2),4,2,1))
title <- paste ("GSE32025", '/', annotation(gset), " selected samples", sep ='')
boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)

jk

Kevin

• 1 views • link
written by Kevin Blighe Kevin Blighe

Thank you very much Kevin!

• 1 views • link
written by elb elb

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