[BioC] NuID conversions

[Pan Du]

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:
http://www.bioconductor.org/packages/2.3/data/annotation/html/lumiHumanIDMap
ping.db.html

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.


Pan



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
> 
>