Hi Jubao The reason of the warning message is that Illumina HT-12 v4 have some new probes not included in previous versions. We will include Illumina HT-12 v4 in the ³lumiHumanAll.db² in the next Bioc release. If your data included annotation information, you can try run lumiR without providing probe mapping library, basically set ³lib.mapping = NULL². Then you can retrieve the annotation information (if included in your data) using command pData(featureData(x.lumi)). You may also just ignore the warning messages because the missing probes are not many. If the missing probes are coincidentally significantly differentiated, then you have to manually annotate it based on Illumina manifest file, which can be downloaded from Illumina: http://www.illumina.com/support/annotation_files.ilmn Have a nice weekend Pan On 7/1/10 7:04 PM, "jubao Duan" <jduan69@gmail.com> wrote: > Hi Pan, > > Does the current Lumi support Illumina HT-12 v4? It worked perfectly with my > v3 array data, but when I tried to annotate probes with nuID for v4 array data > , many nuID could not be annotated with a Warning message: > ³In getChipInfo(nuID, lib.mapping = lib.mapping, species = species, : Some > input IDs can not be matched!². > > Any suggestions to solve this problem? > > Thanks, > > Jubao > [[alternative HTML version deleted]]