Hi Mali First of all, the message you showed is not error. It is just a warning message. There are several background correction methods to select, and the step of background correction itself is optional. The VST transformation can handle the data without background correction. The main affect of without background correction for Illumina data is that the fold- change estimation for low expression probes tends to be lower. But actually that is not bad at all because those low expression and high fold-change probes usually is more likely to be false positive. This is my personal opinion for your reference. As for the warning message, I guess the format of your data might be different from the required one. If you would like to, you can send me the control data file. I will have a brief check for you. Hope this is helpful to you, Pan Date: Tue, 8 Mar 2011 09:30:10 +0200 From: mali salmon <shalmom1@gmail.com> To: bioconductor@r-project.org Subject: Re: [BioC] Lumi problem > Hi All > I am analysing illumina array data using "Lumi", and I found a problem with > adding control data to Lumi. > I have tried: > > >addControlData2lumi("illuminaControls.txt",x.lumi) > and got the following message: > "Annotation columns are not available in the data". > > Then I tried to create the LumiBatch by specifing the mouse annotation > library > >x.lumi<-lumiR("illuminaAll.txt",lib="lumiMouseAll.db") > >addControlData2lumi("illuminaControls.txt",x.lumi) > > but it didn't help, when I try to do background correction, I still get the > error: > "There is no control probe information in the LumiBatch object! > No background adjustment will be performed." > > Any ideas? > Thanks > Mali > [[alternative HTML version deleted]]