Search
Question: Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
0
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.

> 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.

modified 4 months ago by Gordon Smyth35k • written 4 months ago by hks041800
0
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)
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.