[BioC] lumi: target ids versus probe ids?

Michal Blazejczyk michal.blazejczyk at mail.mcgill.ca
Thu May 22 17:30:06 CEST 2008


I have a question regarding best practices of the analysis of Illumina
data using lumi, more specifically - regarding targets vs probes.
In noticed that when I import probe-level data using lumiR(),
and them normalize them, I still end up with probe-level data.
Are there any "summarization" methods for Illumina data?  I mean,
when I have expression values for multiple probes from the same
target, how should I treat them?  The "gene profile" format in
BeadStudio simply takes a mean of all probes that come from the
same target.  Is this the right thing to do?  Should it be done
before or after normalisation?  Or should I ignore target ids
when I have probe-level data?

Best regards,
Michal Blazejczyk

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