[BioC] Merging microarray datasets

[Adaikalavan Ramasamy]

This is an interesting question and one that I like to explore further.

The papers I have seen on combining microarray datasets so far select 
one algorithm for Affymetrix and one algorithm for cDNA.

Has anyone investigated which combination of preprocessing algorithm(s) 
make data from these two platforms comparable? Indeed, how does one 
check if they are comparable? Any references and suggestions would be 
very welcome.

Thank you.

Regards, Adai




Kathy Duncan wrote:
> 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
>
> - - -  - -
>
> Robert Gentleman <rgentlem at 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
>
>
>
> - - - - -  - -
>
> Balasubramanian Ganesan <balag at 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
>
> 	[[alternative HTML version deleted]]
>
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