[BioC] Combining data from runs

Michal Okoniewski michal.okoniewski at fgcz.ethz.ch
Sun Sep 12 18:13:34 CEST 2010

As an alternative to limma in case of batch effect, you may try pamr.batchadjust(), works quite well for me, see also eg: http://www.biomedcentral.com/1755-8794/1/42


-----Mensaje original-----
De: bioconductor-bounces at stat.math.ethz.ch en nombre de Supriya Munshaw
Enviado el: vie 10/09/2010 10:53
Para: bioconductor at stat.math.ethz.ch
Asunto: [BioC] Combining data from runs
We're using Affymetrix HG-U133_Plus_2 arrays and our experiment was done so that 8 of our samples were run initially as a test run, followed by running the remaining 74 samples. Since these were two different runs, I'm pre-processing them differently i.e. running rma on them separately. Is there a way to combine the two datasets after their probe level intensities have been normalized within each run since I want to include the initial 8 samples for differential gene expression analysis? If not, what is the best way to include the 8?
Please let me know.

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