[BioC] lumi: target ids versus probe ids?

[Michal Blazejczyk]

Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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.

> Sean


Hi Sean,

Actually, I was inquiring on the difference between probe- and
gene-level data.  Bead-level data does not really interest me
at this point.  BeadStudio never displays bead-level data, but
it displays both probe-level data and gene-level data.

Thanks,
Michal