Hi Mali The "illuminaControls.txt" file you sent me can be loaded by getControlData function without any problem. The message: "Annotation columns are not available in the data" is the print out message by lumiR function (called by getControlData function). It's not a warning message, just providing some feedback information to the users. Pan 2011/3/8 mali salmon <shalmom1@gmail.com> > Thanks Pan for your reply. > I thought the step for background correction is optional because Lumi > assumes the data is already background corrected (according to the user > guide). I didn't realize that background correction for illumina data is not > a very good idea, thanks for clarifying this. > I compared the file I have (attached) with the sample control file in Lumi, > and they seem to have the same format. > Mali > > > > On Tue, Mar 8, 2011 at 5:15 PM, Pan Du <du4pan1@gmail.com> wrote: > >> 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 >> > >> > > > > -- > Mali Salmon-Divon PhD > EMBL European Bioinformatics Institute > Wellcome Trust Genome Campus > Cambridge CB10 1SD > tel +44 (0)1223 494444 > fax +44 (0)1223 494468 > [[alternative HTML version deleted]]

Yes, the data is loaded by getControlData, but when I run lumiB I get the following message: >addControlData2lumi(controls.matrix,x.lumi) >lumiB(x.lumi,method='bgAdjust') "Perform bgAdjust background correction ... There is no control probe information in the LumiBatch object! No background adjustment will be performed." Thanks Mali On Tue, Mar 8, 2011 at 6:06 PM, Pan Du <du4pan1@gmail.com> wrote: > Hi Mali > > The "illuminaControls.txt" file you sent me can be loaded by > getControlData function without any problem. The message: "Annotation > columns are not available in the data" is the print out message by lumiR > function (called by getControlData function). It's not a warning message, > just providing some feedback information to the users. > > Pan > > > 2011/3/8 mali salmon <shalmom1@gmail.com> > > Thanks Pan for your reply. >> I thought the step for background correction is optional because Lumi >> assumes the data is already background corrected (according to the user >> guide). I didn't realize that background correction for illumina data is not >> a very good idea, thanks for clarifying this. >> I compared the file I have (attached) with the sample control file in >> Lumi, and they seem to have the same format. >> Mali >> >> >> >> On Tue, Mar 8, 2011 at 5:15 PM, Pan Du <du4pan1@gmail.com> wrote: >> >>> 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 >>> > >>> >> >> >> >> -- >> Mali Salmon-Divon PhD >> EMBL European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Cambridge CB10 1SD >> tel +44 (0)1223 494444 >> fax +44 (0)1223 494468 >> > > -- Mali Salmon-Divon PhD EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD tel +44 (0)1223 494444 fax +44 (0)1223 494468 [[alternative HTML version deleted]]