Hello!
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 gcrma
:
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?
Thank you!
Thank you for sharing that very useful workflow, and for clarifying some of the differences between Illumina and Affy arrays.
The problem I'm running into now is that
read.maimages
is looking for columns for two colors. Would theVALUE
column in the OP correspond to the raw intensity of a single color array, or has this file from GEO already undergone some normalization? At what step in the workflow would this be the equivalent of? I've tried to run:And have gotten:
Sorry for the basic questions, I've been scouring the internet and can't seem to get the answers I'm looking for. Thank you for the help!