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 P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.