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

[Maria Jose Nueda]

Dear Maciej,

You can apply maSigPro with 7 time-points without splitting the data. The
method is going to work well. You must split the data if the obtained models
don't fit very well. Splitting the data is not implemented automatically in
the maSigPro R-program and you have to elaborate a more complicate design.
We have developed a web-service where we have implemented maSigPro and other
tools http://sea.bioinfo.cipf.es/. We have tried to simplify things. If you
want apply maSigPro easily you can use it. We are checking that all work
well. If you use it you could send your opinion. You can visit the "help" to
see examples: data and results.

Regarding your question, it is not necesary to use log-ratio (time_point to 
time_zero on each microarray) to apply maSigPro.

On the other hand ASCA-genes is also a methodology to detect significant
genes. We are developing an strategy based on ASCA to eliminate the bacth
effect. This is a preprocessing technique but it is not a normalization
method. We haven't  published anything about this yet. Where did you hear
about it?When we finish all the things we will add in SEA web-service also
this tool.
Best wishes,

María.

----- Original Message ----- 
From: "Maciej Jończyk" <mjonczyk at biol.uw.edu.pl>
To: <bioconductor at stat.math.ethz.ch>
Cc: "Maciej Jończyk" <mjonczyk at biol.uw.edu.pl>
Sent: Tuesday, April 20, 2010 1:48 PM
Subject: [BioC] [maSigPro] How to analyze 2-colour microarrays?


> 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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