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Question: Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
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gravatar for hks04180
4 months ago by
hks041800
hks041800 wrote:

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.

ADD COMMENTlink modified 4 months ago by Gordon Smyth35k • written 4 months ago by hks041800
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gravatar for Gordon Smyth
4 months ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

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 COMMENTlink modified 4 months ago • written 4 months ago by Gordon Smyth35k

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

ADD REPLYlink written 4 months ago by hks041800
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