[BioC] lumi: target ids versus probe ids?

Sean Davis sdavis2 at mail.nih.gov
Thu May 22 17:35:44 CEST 2008

On Thu, May 22, 2008 at 11:30 AM, Michal Blazejczyk
<michal.blazejczyk at mail.mcgill.ca> wrote:
> Hello,
> 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?

Hi, Michal.  You might want to take a look at the beadarray package
which has methods for normalizing and summarizing bead-level data.
The lumi package is designed for pre-summarized data from beadstudio.
The lumi authors could also comment, here.


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