[BioC] NuID conversions

Pan Du dupan at northwestern.edu
Wed Sep 3 00:08:39 CEST 2008

Hi Merja,

We have developed the Illumina IDMapping Metadata packages for this kind of
conversion. For Human, you can use the lumiHumanIDMapping.db package in
developing version of Bioc 2.3:

For more details, please read the " IlluminaAnnotation.pdf" vignette in the
lumi package (developing version 1.7.20).

For example:

You can use nuID2probeID function in the :
  nuID2probeID(nuID, lib.mapping = "lumiHumanIDMapping.db")

Tell me if you have any questions.


On 9/2/08 11:31 AM, "Merja Heinaniemi" <merja.heinaniemi at uni.lu> wrote:

> Dear Pan,
> Two simple questions but I just stumbled on these trying to finish my
> analysis:
> 1) I wanted to make a simple NuID to probeID conversion, my data is Illumina
> Human v3. I got an error message that LumiHumanAll.db does not support the id
> conversion. Is this true or am I just doing sth wrong?
> 2) If I have a vector with ProbeIDs that I am interested in and a normalized
> LumiBatch object from this same Illumina array type, how do I take out from
> the whole dataset just expression values for the specified ProbeIDs?? I want
> to make a heatmap from data of these probes (this set of probes was sign
> regulated under my comparisons).
> Kind regards,
> Merja Heinäniemi

More information about the Bioconductor mailing list