[BioC] ComBat() -- run with one sample in one batch

Peter Langfelder peter.langfelder at gmail.com
Fri Jun 6 20:56:45 CEST 2014

On Fri, Jun 6, 2014 at 11:43 AM, Guest [guest] <guest at bioconductor.org> wrote:
> Hi,
> Is there a work around for ComBat() where I can run the function if I have only one sample in one batch?

No. ComBat adjusts location (mean) and scale (variance) for each
batch. There's no way to estimate/adjust scale with just one sample in
a batch.

> I'm working with affymetrix, human chip U133A and trying to remove batch effect on scan date. I have some samples that were scanned individually on separate dates. So there are some dates where only one sample was run.
> Any insight regarding this will be appreciated.

Produce a sample clustering tree to see how different the samples
scanned on close dates are - often they are not very different and can
be combined into a single batch (not ideal but better than nothing).
Make sure the resulting batches are not completely confounded with
your variable of interest (treatment or condition).


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