Thank you Maciej, your experience is really helpful. I'll try to add higher 
orders step by step.

-Xiaokuan




________________________________
From: Maciej Jończyk <mjonczyk@biol.uw.edu.pl>

Cc: Maciej Jończyk <mjonczyk@biol.uw.edu.pl>
Sent: Wed, August 18, 2010 4:38:51 AM
Subject: Re: [BioC] Long Time Series analysis

Dear Xiaokuan,



> Date: Wed, 11 Aug 2010 21:12:04 -0700 (PDT)



> To: bioconductor@stat.math.ethz.ch

> Subject: [BioC] Long Time Series analysis

>

> Dear List,

>

> I?was using?maSigPro for time series analysis of microarray.?I

> have about 12

> time points for a yeast data, and each time point only has two

> replicates. I am

> wondering if I can use quadratic model?to perform the analysis. If I

> used higher

> order model, will overfitting become a problem?



I've done analysis of time-course experiment with seven points, I
considered to use 3rd or 4th order polynomial. Eventually it turned out
that 3rd order is enought, 4th order gives nothing new.

I advise you to try with quadratic model, 3rd, 4th and maybe higer order
polynomial too and to look if it gives different results, if not lower
level polynomial is enought.





>

> I noticed that in?maSigPro tutorial, 4.4 mentioned "Long Time

> Series". But it

> has no detailed explaination. Does Ana or someone can share?some

> examples I can

> follow for such analysis?



I've asked for longer than mentioned 5 time points series and I've been
informed that in case of 7 time points I can use normal workflow.

>

> Any other packages I can use for a long time series analysis?



You can look in "packages" section at the Bioconductor website.

Hope it helps somehow.



> Your help will be greatly appreciated.

>

> Thanks again.

>

> Regards,

> Xiaokuan

>

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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