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maSigPro (version 1.49.3.1+galaxy0)

Choose data source:

Choose if you want to provide seperate count files (e.g. from HTSeq-count or feature-seq) and define your experiment design matrix here, or if you have maSigPro edesign and data input files already.

Experiment matrix:

Matrix describing experimental design. Rows must be arrays and columns experiment descriptors

Gene expression matrix:

Matrix containing normalized gene expression data. Genes must be in rows and arrays in columns

Column number containing time values:

Column number in edesign containing time values. Default is first column

Column number containing replicate coding:

Column number in edesign containing coding for replicate arrays. Default is second column

Step 1: make.Design.Matrices - Defining the regression model

Step 1: make.Design.Matrix - Defining the regression model 0

Step 2: p.vector - Finding significant genes

Step 2: p.vector - Finding significant genes 0

Step 3: T.fit - Finding significant differences

Step 3: T.fit - Finding significant differences 0

Step 4: get.siggenes - Obtaining lists of significant genes

Step 4: get.siggenes - Obtaining lists of significant genes 0

Generate visualization PDF:

Choose if you want to generate a PDF file containing the visualizations

Step 5: see.genes - Visualizations

Step 5: see.genes - Visualization 0

What it does

maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.

Inputs

The maSigPro wrapper has two options for input data:

directly through two seperate text files containing the experiment design (edesign) and the data or

count tables generated from HTSeq-count. Count tables must be generated for each sample individually.

To set up an experimental design from seperate count files you first have to select which files belong to a certain time point. Likewise you can specify which files are replicates. In a third step you have to create the experimental groups and select the related files. For a more comfortable setup in future analysis you have the option to output the generated edesign and data files.

Output

maSigPro generates a summary file containing the list of significant genes. Additionally you can obtain a PDF file containing plots of profiles and groups that visualize the clustering analysis.