Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
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hks04180 • 0
@hks04180-16100
Last seen 5.8 years ago

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 • 2.2k views
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@gordon-smyth
Last seen 17 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. 

 

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

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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$E
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UnloggedExpression <- 2^yr$E
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Dear Gordon Smyth thank you very much the prompt response.

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