Hi list,

We have recently seen an odd distribution of signal intensities using the
new version 4 HT-12 chips. Specifically, the distribution of negative
controls looks like a mixture of two gaussians. This invalidates the common
assumption of normal distributed background used in both  the detection
calls and some error-model based normalizations, e.g. norm-exp in limma. We
did not have this type of distribution in version 3 of HT12, nor in any
other chip type from Illumina. Has anyone else seen this particular issue,
and specifically on the HT-12 v4 chip?

Below is a link to density plots of the negative control probes of 6
experiments I've compared. The top plots are from a lab in Oslo on the HT-12
v4, at hte bottom are two experiments from our lab using HT12 v4 and a
comparison of a Rat v1 chip from our lab.

Figure:
http://oi52.tinypic.com/tz05v.jpg <%20http://oi52.tinypic.com/tz05v.jpg>


Thanks,

Arnar


----------------------
Arnar Flatberg
Data scientist
Trondheim Genome Resource Center
St. Olav's hospital, Norwegian University of Science and Technology
Trondheim
Norway

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