\HeaderA{masigpro.edesign}{The function creates an edesign object needed to run maSigPro}{masigpro.edesign}
\keyword{utilities}{masigpro.edesign}
\begin{Description}\relax
The function creates an edesign object needed to run maSigPro. To know more about edesign object 
see maSigPro help. 
This function uses a specific configuration of Target column of the affylmGUI target file.
To know more about target file see affylmGUI help.
Each row of the column named Target, in the affylmGUI target file, describes the array on the basis
of the experimental design.
Each element needed for the construction of edesign is separated from the others by an underscore. 
The first three elements of the row are fixed and represent Time Replicate Control all separated by an underscore:
\verb+Time_Replicate_Control+ .
All the other elements refer to various experimental conditions.
Considering two different conditions to be evaluated each row is made of 5 elements:
\verb+Time_Replicate_Control_cond1_cond2+ all separated by an underscore.
Having an experiment made of 9 arrays, with two time points, 0h and 24h, in triplicate, and two different
experimental conditions to be evaluated, the affylmGUI target file will look like:
Name   FileName        Target
mC1    M1.CEL  \verb+0_1_1_0_0+
mC2    M4.CEL  \verb+0_1_1_0_0+
mC3    M7.CEL  \verb+0_1_1_0_0+
mE1    M3.CEL  \verb+24_2_0_1_0+
mE2    M6.CEL  \verb+24_2_0_1_0+
mE3    M9.CEL  \verb+24_2_0_1_0+
mI1    M2.CEL  \verb+24_3_0_0_1+
mI2    M5.CEL  \verb+24_3_0_0_1+
mI3    M8.CEL  \verb+24_3_0_0_1+
\end{Description}
\begin{Usage}
\begin{verbatim}masigpro.edesign()\end{verbatim}
\end{Usage}
\begin{Author}\relax
Raffaele A Calogero
\end{Author}
\begin{SeeAlso}\relax
masigpro, masigpro.view
\end{SeeAlso}

