[BioC] cellHTS2 - 2 channel batch analysis

[Steve Taylor]

Hi,

I am trying to set up a two channel analysis using cellHTS2.

I have cell line X. X has control (C) and experiment (E) conditions. The screen uses 3 x 96 well plates and C and E have 2 replicates each, hence C and E have 6 plates each in total.

It gets complicated because there is a repeat of the whole experiment (on a separate day) and the experimenter used a different plate configuration. Also 3 of the control plates were not run, so for 
the second experimental run C has 3 plates and E has 6 plates.

I'd like to combine both experiments but wondered what is the best way? I read you can normalize for batch effects which looks like it should help but on the whole I am unsure how to configure this 
analysis.

Thanks for any help,

Steve
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Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University