[BioC] batch effect confounded with condition

[Moshe Olshansky]

Dear Tefina,

Since condition and time batch are completely confounded, strictly
speaking there is no way do distinguish between the affect of the
condition and the batch. So no software package can help.
However, if you have negative controls, i.e. genes which should not be
affected by condition (including manufacturer's control genes) you can try
to use them to estimate (and at least partly remove) batch effect.

Best regards,
Moshe.

> Dear List,
>
> I have microrarray data where condition is completely confounded with a
> time
> batch effect. When doing a PCA on the RMA normalized data, the first
> principal
> component separates clearly the two batches.
>
> What option do I have when I still want to compare different conditions
> across
> batches?
> As far as I understood I can't dissolve this batch effect neither with
> limma nor
> with e.g. ComBat.
> Shall I just go on with the limma analysis and keep in mind that some
> genes just
> might pop up due to batch effects?
>
> best,
> tefina
>
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