Anova (version 1.2.1)

Data Matrix file:

Matrix of numeric data with headers.

Sample Metadata file:

Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition

Variable Metadata file:

Tabular file with information about your tested variables. Only used to aggregate generated information.

Mode:

Perform the anova tests on column/row; for W4M 3-tables format, use 'row'.

Condition:

The column name of the condition. ex: hour or treatment

Conditions for N-ways anovas

Conditions for N-ways anova 0

Enable interaction response p-values:

Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)

PValue adjusted method:

Method used to apply a correction on the pvalue because of the number of test

Threshold:

max adjusted p.value accepted

Selection method:

Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold.

Separator of columns:

Decimal separator:

Authors Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr Melanie Petera - PFEM ; INRA ; MetaboHUB

Anova

Description

Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures, in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.

Note about sum of squares (SS) calculation of N-way ANOVA in this module. This module use R function manova() (and thus R function aov()) to establish N-way ANOVA. Therefore calculated sum of squares are sequential ones (sometimes called "Type I SS"). If your design is unbalanced, this may not correspond to the type of hypothesis being of interest. Note that you can obtain adjusted sums of squares ("Type II SS") by running several times this module with different orders in factors.

Input files

Parameter : num + label	Format
1 : Data Matrix file	Tabular
2 : Sample Metadata file	Tabular
3 : Variable Metadata file	Tabular

Output files

*.anova_pvalue.tabular

Your variable metadata file completed with columns of p-values, result of selection method and means of subgroups.

*.anova_signif.pdf

A pdf file containing a Venn diagram and boxplots of significant variables.

The outputs *.anova_filtered.tabular is a tabular file. You can continue your analysis using it in the following tools:

Generic_filter

Hierarchical Clustering