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
> 




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