Table of Contents 

maxLevel  2 

minLevel  2 

exclude  Additional Assistance 


The Nonparametric ANOVA task uses the KruskalWallis and Dunn's tests (Nonparametric ANOVA) task is used to identify deferentially expressed genes among two or more groups. Note that such rankbased tests are generally advised for use with larger sample sizes.
Running the task
To invoke the NonKruskalparametric ANOVAWallis test, select any countbased data nodes, these include:
 Gene counts
 Transcript counts
 Normalized counts
Select Nonparametric ANOVA under the Statistical analysis section of the context Statistics > Differential analysis in the contextsensitive menu, then select KruskalWallis (Figure 1).
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SubtitleText  Select any count node to invoke the Nonparametric ANOVA task 

AnchorName  Nonparametric ANOVA 


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Select a specific factor for analysis and click the Next button (Figure 2). Note that this task can only take into account one factor at a time.
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SubtitleText  Select one factor for analysis 

AnchorName  Nonparametric_factor 


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For more complicated experimental designs, go back to the original count data that will be used as input and perform Rank normalization at the Features level (Figure 3). The resulting Normalized counts data node can then be analyzed using the Detect differential expression (ANOVA) task, which can take into account multiple factors as well as interactions.
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SubtitleText  Normalize your count data by rank to do nonparametric testing on more complicated experimental designs 

AnchorName  Rank_normalization 


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Define the desired comparisons between groups and click the Finish button (Figure 4). Note that comparisons can only be added between single group (i.e. one group per box).
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SubtitleText  Setup desired comparisons 

AnchorName  Nonparametric_comparisons 


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Report
The results of the analysis will appear similar to other differential expression analysis results. However, the column to indicate mean expression levels for each group will display the median instead (Figure 5).
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SubtitleText  The task's ANOVA report will display the median instead of the LSmean 

AnchorName  Nonparametric_report 


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