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

[Maciej Jończyk]

Dear María,

thank you for response

Maria Jose Nueda <mj.nueda at ua.es> nadawca :

> 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.

Ok, I'll try analyze my data without splitting and I'll see how it
works.

> 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.

I want to try analysis in R first, but I'll look on this site.

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

This question was inspired by the form of design file. In the
"maSigPro-tutorial.pdf" you gave examples. I've thought that there is
only one row per array (in other case name of each array was written two
times - for sample labeled with cy3 and cy5, respectively), so I thought
that data must be in log-ratio form.
What is the correct form of design file for data in log2(fluorescence)
form?

> 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?

I've read about it in your doctoral thesis, which I 've found on the
internet.
I've found it an interesting method, and the tesis is very inspiring.
Now I want to use ASCA-genes as a preprocessing technique for subsequent
analysis in maSigPro, and I wonder how could I transport objects between
this two packages.

Best wishes,
Maciej



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