I have some Illumina Bead Array data from a publication, and I'm struggling to properly analyze them. The data are deposited in GEO, and the arrays were performed on
Illumina HumanWG-6_V2_0_R2 and
Illumina HumanWG-6 v2.0 expression beadchip. All of my experience is with Affy, so this may be a case of user error.
As opposed to a
.cel file, these data are uploaded as
.txt files. For example:
ID_REF VALUE Detection Pval ILMN_1762337 6.061683178 0.6073781 ILMN_2055271 6.506861687 0.03162055 ILMN_1736007 6.121051788 0.4624506 ILMN_2383229 5.960764885 0.8155468
I've generated density plots of the signals in the
VALUE column across multiple samples, and the density plots are very divergent, indicating that these are raw data I'm looking at (the manuscript and GEO entry were unclear).
My goal is to perform
gcrma normalization, then analyze these data via
limma. The issue I'm running into is that when I use
read.table to import these data I receive errors when I try to run
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘indexProbes’ for signature ‘"data.frame", "character"’
What's the best way to import, normalize, and analyze array data from a
.txt file using limma?