Welch's ANOVA

Welche's ANOVA is similar to one-way ANOVA, but it doesn't have equal variance assumption. It applies to data with an attribute has more than two groups, but the variances among the groups are not equal. It is based on weighted means. When the attribute has only two groups, it is equivalent to the unequal variance t-Test (also known as Welch's t-Test).

Running the task

To invoke Welch's ANOVA, select any count-based data nodes, these include:

• Gene counts

• Transcript counts

• Normalized counts

After clicking on the chosen node:

• Select Statistics > Differential analysis in the context-sensitive menu.

• Select Welch's ANOVA.

• Select a specific factor for analysis and click the Next button to setup the comparisons.

• Define the comparisons by dragging and dropping each group in the Denominator and Numerator boxes and click Add comparison

If the data has not been filtered upstream the Low value filter box will be checked by default. Similarly, the Default normalisation will be selected if the software detects that the data as not been previously normalised.

Advanced option

Advanced options configuration allows to choose different multiple test correct and report options

The results of the analysis will appear similar to other ANOVA/LIMMA-trend/LIMMA-voom. However, the column to indicate mean expression levels for each group will display the median instead for Kruskal-Wallis.