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Serge Eifes
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@serge-eifes-2032
Last seen 10.2 years ago
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