[BioC] Between array normalization for biological replicates

[Wolfgang Huber]

Dear Serge,

> Recently we have performed a microarray time-scale experiment including
> different time-points (0h, 2h, 6h, ...). Treated and untreated cells were
> compared by competitive hybridizations for every time-point using
> dual-channel microarrays. Every time-point was performed in triplicate
> including 3 biological replicates.
> 
>  Comparing the boxplots for the three biological replicates on  every
> time-point it seems as the data distribution is quite different between the
> replicates. In such a case, if I understood right it might sometimes be
> worth to perform between array normalization by ....

Since you say "replicates"...: Another action that might be worthwhile 
in such a case is to carefully look at scatterplots, histogrammes, 
spatial plots of the data and to carefully consider the question whether 
the data quality is appropriate for the intended analysis.

Best wishes
   Wolfgang

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber