[BioC] What should happen to control probe information in bead level Illumina analyses?

[Johnstone, Alice]

Hi again!

When running through my analysis of bead summary data that I have
created from bead level data (background corrected with normexp, and
summarised standard) I produced a topTable list which contains probeIDs
that are not found in Illumina's reference file.  When I checked the
controlprobeprofile.txt there they were!
It looks like I haven't got huge DE change in my experiment, but I still
wouldn't have expected Illumina's negative controls to make the top 50..
Somethings not right.

So the question is: should I be creating my own controlprobe file from
bead level data, as I background-corrected my data in a non-standard
manner? This would make a difference to the control probes as well,
correct or is it marginal?
Would it be necessary to incorporate it into my BSData object also?  


Thanks for your time.

Regards,

Alice Johnstone

PhD Student
Institute of Environmental Science and Research Ltd
Kenepuru Science Centre
34 Kenepuru Drive
PO Box 50-348
Porirua
New Zealand

Tel:  + 64 4 914-0717
Fax: + 64 4 914-0770


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