[BioC] lumi: target ids versus probe ids?

[Sean Davis]

On Thu, May 22, 2008 at 11:44 AM, Michal Blazejczyk
<michal.blazejczyk at mail.mcgill.ca> wrote:
> 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.

Ahh, sorry about that.  Use the probe-level data, yes.  There is not a
real advantage that I can think of for summarizing to genes at any
point during an analysis, as the probes are potentially measuring
different things even though they are supposed to be measuring the
same gene expression.

Sean