Thanks Robert & Balasubramanian!

Let's consider that the raw datasets (of a platform) are individually
normalized. Now, what approach is advisable to have a single set out of them
while they are scaled too to get rid of the possible "between-array"
variation (I hope this sounds ok !).

Kathy

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Robert Gentleman <rgentlem@fhcrc.org> wrote:

Hi Kathy,
 This question has been asked many times, and the advice remains the same:
it doesn't make any sense to normalize different data sets together.  You
should normalize them separately and use appropriate statistical models to
combine the data into a single analysis.

best wishes
 Robert



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Balasubramanian Ganesan <balag@cc.usu.edu> wrote:

Yes, but you have to normalize all raw data together. All data should also
be of one platform only. Then you can simply normalize all CEL files or all
----- files together and be done.
For Affy data, you can use the Affy package for normalization. Depends on
how you want to normalize anyway.


------------  Original Message ---------------------



Kathy Duncan wrote:

Hi,

I have a simple and basic question:

Is it alright to think of merging two datasets (either from cDNA or
Affymetrix platform) - Final goal is to have ONE normalized dataset, where
the datasets are scaled in order to compensate the different types of
variations, if present !

Comments on strategy and packages available in Bioconductor would be of
great help.

Thanks.

Kathy

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