I have a few questions about using human samples with the Illumina HumanHT-12 v4 BeadChip. I would like to use an external RNA spike-in control to normalize my samples when comparing differential gene expression between conditions.
1) Is it possible/necessary to use ERCC RNA spike-in mixes with Illumina BeadChips? I notice that there are internal quality controls on the chip labeled with the ERCC probes. Does this mean that those spike-ins are already built into the hybridization master mix? Will I gain anything useful if I add my spike-in to my samples?
2) How do I normalize my expression data to external controls at the R Bioconductor/lumi/limma level?
I appreciate any help or points to the right direction!