[BioC] [maSigPro] How to analyze 2-colour microarrays?

[Maciej Jończyk]

Dear List Members,

First - my experiment

I have 7 time points and two treatments (cold and control).
I used two-colour microarrays, each RNA was hybridized with a common
reference (time zero).

I've searched list's archive and read the tutorial but still I can't
figure out how can I analyze this experiment (two-colour with common
reference) in maSigPro.
I know that I have to split my data (long time series).

I'd like to make two variants of analysis:

1 - Normalization in limma, analysis in maSigPro.

2 - ASCA-genes, then analysis in maSigPro (normalization?).

My questions are:

(1) - Should I use log-ratio (time_point to time_zero on each
microarray) in analysis?
(2) - How experimental design file should look like in this case?

I've read about ASCA-genes methodology, which can be used as a
preprocessing method to subsequent analysis in maSigPro. I've found
codes but I don't know how the results from ASCA-genes can be passed to
maSigPro.

Should I normalize the data before using ASCA-genes?

Help will be very appreciated.
Best Regards,

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



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