[BioC] Distribution of negative controls on Illumina HT12-v4 chips (double background?)

[Wei Shi]

Dear Arnar:

	Thanks for the detailed report for the intensity distributions of negative control probes in your data. But could you please provide more information about the numbers of different types of probes? If you used the limma function read.ilmn to read in your data, you can get this information by this command:

table(x$genes$Status)

	Also, it will be a lot helpful if you could provide your code for creating the density plots.

Thanks,
Wei


On Feb 23, 2011, at 1:46 AM, Arnar Flatberg wrote:

> 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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