I am using lumi to process data from Illumina HT-12 v3 Expression BeadChips. I am slightly concerned about the average number of bead replicates present on the Illumina HT-12 chip, as opposed to the Illumina WG-6 chip. Each bead is replicated on average 15 times on the Illumina HT-12 chip, as compared to an average of 30 times on the HumanWG-6 chip.
Would you still suggest using VST with the Illumina HT-12 chip data, given the number of bead replicates?
Thanks for your help.