Question

Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package

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Harpreet Kaur • 0

@hks04180-16100

Last seen 4 months ago

United States

I am trying to process GEO series, like GSE36411 data (Illumina data) using lumi package and limma package.

I am getting following following error for above mentioned series and for many such series.

> raw.data <- read.ilmn(files="GSE36411_non-normalized.txt")
Reading file GSE36411_non-normalized.txt ... ...
Error in readGenericHeader(fname, columns = expr, sep = sep) :
Specified column headings not found in file
> abc1 <- lumiR("GSE36411_non-normalized.txt", lib.mapping = 'lumiHumanIDMapping')
Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds

Can anyone suggest me the reason for this and how can I solve such issue. or there is any such package is available by which i can process such type of files of Illumina data.

limma lumi illumina gene expression data • 2.8k views

ADD COMMENT • link updated 3.0 years ago by mohammedtoufiq91 ▴ 10 • written 6.5 years ago by Harpreet Kaur • 0

score 1 · Answer 1 · 2018-06-21

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Gordon Smyth 52k

@gordon-smyth

Last seen 52 minutes ago

WEHI, Melbourne, Australia

It works fine for me:

library(limma)
x <- read.ilmn("GSE36411_non-normalized.txt", probeid="ID_REF", expr="GSM")
y <- neqc(x)

The data file has been edited and no longer has standard Illumina column headings, so you have to tell read.ilmn how to recognize the probeid column and the expression columns.

ADD COMMENT • link 6.5 years ago Gordon Smyth 52k

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Thank You Gordon Smyth. It works for me now, earlier I was missing this expr="GSM".

ADD REPLY • link 6.5 years ago Harpreet Kaur • 0

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Dear Gordon Smyth
I am using limma for analyzing Illumina expression microarray datasets and apply neqc function. I could extract the normalized log-intensities, Inaddition, I would like to also obtain unlogged normalized values. Is it possible to extract the data or is there any appropriate function for this?

library(limma)
xr <- read.ilmn(files="non-normalized.txt", probeid="ID_REF", expr="GSM")
yr <- neqc(xr)

## normalized log-intensities
yr$E

ADD REPLY • link 3.0 years ago mohammedtoufiq91 ▴ 10

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UnloggedExpression <- 2^yr$E