[BioC] merging (Combining) microarray datasets on different platforms

[Hui Yu]

In my opinion, you should normalize, at least with regard to the two
different platforms, before attempting to merge duplicated
measurements of identical samples. Most probabably you'll end up
averaging the measurements of the duplicatedly-measured probes, and
collating the measurements for different genes from different
platforms into one single data column. These operations require you
ensure that the measurements from the two separate platforms are
comparable by the time of merging.
You may want to normalize only the platform-specific bias before the
merging; a loess-like calibration based on the 168*50*2 data-points
may suffice for this purpose. You have 168*50 pairs of data-points,
where each pair of data-points, one from GPL3694 and the other from
GPL3696, should be theoretically identical. A loess regression will
suppress the artificial difference between GPL3696 and GPL3694.
After the merging, which resulted in 50 data-columns each
corresponding to a different sample, you can implement whatever
normalization that came up to your mind in ordinary cases. Given the
fact that you have only ~5000 probes on each chip, which account for
only 25% of the total number of human genes, however, it may be
riskful to apply any global normalization that is based on the
'invariable-total-expression' assumption. Maybe you need addtional
information to normalize between samples.
Any other opinions?

On Fri, Jun 19, 2009 at 10:06 AM, LiGang<luzifer.li at gmail.com> wrote:
> Dear list,
>
> I have one question about merging (Combining) microarray datasets.
>
> I have 50 samples, and each sample was hybridized to 2 different platforms---
> GPL3694 (5352 probes) and GPL3696 (also 5352 probes) in duplicate.
> There were 168 probes identical between these two platforms.
>
> I want to merge (combine) two hybridization files of each sample before
> performing normalization for all 50 samples.
> What appropriate method can be used to do this?
> Can the common 168 probes provide some information?
>
> Thanks!
> ---
> LiGang
>
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