masigpro.edesign: The function creates an edesign object needed to run maSigPro

In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

Description

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: 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: 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	0_1_1_0_0
mC2	M4.CEL	0_1_1_0_0
mC3	M7.CEL	0_1_1_0_0
mE1	M3.CEL	24_2_0_1_0
mE2	M6.CEL	24_2_0_1_0
mE3	M9.CEL	24_2_0_1_0
mI1	M2.CEL	24_3_0_0_1
mI2	M5.CEL	24_3_0_0_1
mI3	M8.CEL	24_3_0_0_1

Usage

masigpro.edesign()

Author(s)

Raffaele A Calogero

See Also

masigpro, masigpro.view

oneChannelGUI documentation built on Nov. 17, 2017, 11:02 a.m.