[BioC] Analysing Illumina v2 and v3 platforms

Pan Du dupan at northwestern.edu
Wed Mar 11 16:15:15 CET 2009

Hi Emanuele,

If you want to combine data from different versions of Illumina data, it is
better to convert the Illumina IDs as nuIDs (created based on probe
sequence) because the Illumina IDs may not be consistent across versions and
different Illumina IDs may have the same probe sequences. You can use lumi
package for this purpose. Just subsetting the data with common IDs and do
the normal processing. But you do need to check the possible batch effects.


On 3/11/09 6:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Tue, 10 Mar 2009 11:38:31 +0000
> From: Emanuele Marchi <emanuele.marchi at imm.ox.ac.uk>
> Subject: [BioC] Analysing Illumina v2 and v3 platforms
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <49B65137.9090106 at imm.ox.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Dear All,
> I would like to choose the proper package to analyse (and possibly
> merge) data from Illumina arrays of different designs.
> The probes content of our arrays, Illumina v2 and v3, overlaps of 77%,
> meaning that v3 arrays retains nearly all the probes present in the old
> v2 layout.
> I think the best way might be to analyse the datasets separately using a
> non parametric test, like Rank Product or Wilcoxon rank-sum test, and
> then compare the results.
> Does anyone have a particular suggestion about it?What package and/or
> strategy to use?
> Thanks a lot in advance,
> Kind Regards.
> Emanuele

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