[BioC] Between array normalization for biological replicates

Serge Eifes serge.eifes at lbmcc.lu
Wed Sep 12 17:06:43 CEST 2007


Dear all,

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.

Microarray analysis is performed in R with Limma using linear models (but
not based on a separate channel analysis (mixed models)!!!). 

 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 performing scale
normalization between the three replicates for every given time-point. How
could this be performed best? By splitting up the MAList object into as many
MAList objects as there are different time-points (always grouping together
the three replicates for a time-point into one object)  before performing
between array normalization and then merging it back afterwards into a
single object? Are there other possibilities to perform this? Is it correct
to perform between array normalization for the three replicates on every
time-point as I described here?

Here you may find the corresponding R code:

>#Splitting up MAList object (MA):
>MA.t0 = MA[, 1:3]
>MA.t2 = MA[, 4:6]                                     
>MA.t6 = MA[, 7:9]
>
>#Between array scale normalization for the different time-points :
>MA.t0 = normalizeBetweenArrays(MA.t0, method="scale")
>MA.t2 = normalizeBetweenArrays(MA.t2, method="scale")
>MA.t6 = normalizeBetweenArrays(MA.t6, method="scale")
>
>#Merging normalized data back into a single object for further analysis:
>MA = cbind(MA.t0, MA.t2, MA.t6)

I would appreciate any comments or suggestions.

Regards,
Serge Eifes




Serge Eifes
Laboratoire de Biologie Moleculaire et Cellulaire du Cancer (LBMCC)
Hopital Kirchberg 
9,rue Edward steichen 
L-2540 LUXEMBOURG
Phone:+ 352 2468-4046               Fax : + 352 2468-4060



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