Analysing microarray raw data: GSEXXXX_non-normalized.txt
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mkd12 • 0
@mkd12-14834
Last seen 3.6 years ago

I have been trying to analyse raw microarray data (Illumina HumanHT-12 V4.0 expression beadchip) downloaded from GEO. 

  • Can anyone explain following error and ways to rectify it.
  • Any alternate method will be appreciated. 
  • I would like to have a base corrected, quantile normalised data. 

For information series matrix is already log transformed and normalised so can not use "GEOquery" package.

> biocLite()
> biocLite("lumi")
> library(lumi)
> setwd("R:/xxxx/yyyy/123/RAW files GSE/GSE42826")
> lumi42826<- lumiR("GSE42826_non-normalized.txt", probeid="Probe_Id")
Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds

 

lumi microarray GSE • 512 views
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@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia

I was able to read and normalize the data using the limma package:

> library(limma)
​> x <- read.ilmn("GSE42826_non-normalized.txt",expr="Sample")
Reading file GSE42826_non-normalized.txt ... ...
> y <- neqc(x)
Note: inferring mean and variance of negative control probe intensities from the detection p-values.
> dim(y)
[1] 47323   102

This produces background-corrected, quantile-normalized log2-intensities, using negative controls as described by https://doi.org/10.1093/nar/gkq871

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