Hi Lavinia, Before combining tow dataset of different Illumina chip versions, you need to convert them as the same type of IDs (nuID is a good option provided in the lumi package). Then you should subset the datasets by using the common IDs before combining them. Here is one example: Suppose you have two LumiBatch objects: x.lumi1 and x.lumi2 of Human Illumina chips, you can use the following code: x.lumi1 = addNuID2lumi(x.lumi1, lib=¹lumiHumanIDMapping¹) x.lumi2 = addNuID2lumi(x.lumi2, lib=¹lumiHumanIDMapping¹) commonID = intersect(featureNames(x.lumi1), featureNames(x.lumi2)) x.lumi.combine = combine(x.lumi1[commonID,], x.lumi2[commonID,]) If the library ¹lumiHumanIDMapping¹ cannot be install through biocLite(), you can also use library ¹lumiHumanIDMapping.db¹. These two libraries basically are the same. Also you need to use R 2.8. Tell me if you have further questions. Pan On 11/13/08 7:00 PM, "Lavinia Gordon" <lavinia.gordon@mcri.edu.au> wrote: > Hi Pan, > > I tried to send this email to the Bioconductor list but for some reason it > didn't appear properly on the mailing list. I wondered if you might be able > to help, as I am sure that it is a question that others have asked. > > with thanks for your time, > > Lavinia Gordon. > >> Date: Thu, 13 Nov 2008 15:11:26 +1100 >> To: bioconductor@stat.math.ethz.ch >> From: Lavinia Gordon <lavinia.gordon@mcri.edu.au> >> Subject: Illumina arrays - combining two versions. >> >> Dear all, >> >> I have two sets of data, both generated on Illumina BeadArrays, but on two >> different versions of the array (the newer version has slightly more probes). >> I would like to normalize these two array types together in lumi, does anyone >> know if/how this can be done? >> >> with thanks for your time, >> >> Lavinia Gordon. >> >> ------------------------------------------------------- >> Bioinformatics Department >> Rm SW916, 9th Floor >> Murdoch Children's Research Institute >> Royal Children's Hospital >> Flemington Road, Parkville >> Victoria 3052 >> Australia >> Tel: (+613) 8341 6221 >> ------------------------------------------------------- > ------------------------------------------------------- > Bioinformatics Department > Rm SW916, 9th Floor > Murdoch Children's Research Institute > Royal Children's Hospital > Flemington Road, Parkville > Victoria 3052 > Australia > Tel: (+613) 8341 6221 > ------------------------------------------------------- [[alternative HTML version deleted]]