Hi-

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.

Christina Markunas

cam27@duke.edu

Graduate student

lumi's vst normalization algorithms work fine on HT-12 arrays. The lower number of beads per probe compared with WG-6 should have little influence.

You could also consider the neqc() function in the limma package. See

  http://nar.oxfordjournals.org/content/38/22/e204

for a comparison of the methods.