An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20110301="" 105bf6e1="" attachment.ksh="">

Hi Arnar: Although it is possible that the scanner upgrade could be the cause, but I think this possibility is quite weak. I will be happy to have a look at your control data to see if there is anything unusual with your controls. You can send me your control data only (the control probe profile) off-line if you like. I don't really think Illumina Technical Support can help you on this matter. Cheers, Wei On Mar 1, 2011, at 5:42 PM, Arnar Flatberg wrote: > Hi Gordon, Ina > > > Thank you for your responses, they have been very helpful. We are currently > seeking Illumina techsupport for answers. This might be related to a recent > scanner upgrade. > > > Arnar > > > > On Mon, Feb 28, 2011 at 5:15 PM, Ina Hoeschele <inah at="" vbi.vt.edu=""> wrote: > >> Hi Arnar, Gordon et al., >> we also have data on an increasing number of these chips, and so far I >> see no evidence for a bimodal distribution. >> Ina >> >> >> ----- Original Message ----- >> From: "Gordon K Smyth" <smyth at="" wehi.edu.au=""> >> To: "arnar flatberg" <arnar.flatberg at="" gmail.com=""> >> Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org=""> >> Sent: Saturday, February 26, 2011 11:39:20 PM >> Subject: [BioC] Distribution of negative controls on Illumina HT12-v4 chips >> >> Hi Arnar, >> >> Wei Shi and I have checked out our own HT-12 v4 data, and we do not see >> the bimodal distribution that you have observed. So we think that this >> might be a property of your data rather than a property of HT-12 v4 >> BeadChips in general. >> >> Note that we are now recommending the neqc() function of the limma package >> for background correcting and normalizing Illumina arrays. This is a >> modication of the normexp algorithm to use negative control probe >> estimates. See ?neqc and the Illumina case study in the limma User's >> Guide. This function will not be very sensitive to the shape of the >> distribution of the negative controls. >> >> Best wishes >> Gordon >> >> >> >> ------ ORIGINAL MESSAGE ------- >> [BioC] Distribution of negative controls on Illumina HT12-v4 chips >> (double background?) >> Arnar Flatberg arnar.flatberg at gmail.com >> Tue Feb 22 15:46:45 CET 2011 >> >> 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 >> >> ______________________________________________________________________ >> The information in this email is confidential and inte...{{dropped:13}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}