anova-twoway-withrep

Synopsis

Does a two-way analysis of variance. The model includes main and interaction effects. The data must be from a balanced design with equal replicates.

anova-twoway-withrep [-l: log transform; -v: verbose output; -r: format line needs to be removed] <data> <layout>

Inputs

• data: A tab-delimited data file, where each row represents a set of measurements to be analyzed. A p value is generated for each row in the file. See the detailed instructions for the format.
• layout: A simple file describing the experimental design. See the documentation of the format.

Outputs

The following columns will be present at minimum. If you select 'verbose' output, more columns will be present.

• The gene identifier
• The F statistics (ff = first factor; sf = second factor; sxf = interaction between first and second factors)
• The p values.

Options

• -r: The data file includes an extra line after the first line. (See the data format page for an explanation)
• -l: Use the log transformation of the data. Do not use this if your data includes non-positive values.
• -v: Provide more verbose output.

Dependencies

• Stats.pm
• This isn't a dependency, but gnu sort is useful for processing the output.

Problems/bugs

• Only works with balanced designs (equal replicates)
• Need better checking for valid layout.

Version history

References