Lumi, HT-12 chip, and number of bead replicates
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@christina-markunas-3378
Last seen 8.1 years ago

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 • 1.1k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

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.

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