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How to Streamline RNA-Seq analysis and increase productivity—point, click, and done
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Feature many-to-one correlation
Only numeric factors are available. When multiple numeric factors are added, the correlation analysis will perform each factor with a feature in the data node independently. If you are interested in particular features, use the Search features box to add one or more.
- Select the factors and interactions to include in the statistical test (Figure 2).
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Correlation analysis produces a Correlation data node; double-click to open the task report (Figure 3) which is similar to the ANOVA/LIMMA-trend/LIMMA-voom and GSA task reports and includes a table with features on rows and statistical results on columns.
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Each feature includes chromosome view, dot plot, correlation plot, and extra details buttons in the View column.
Correlation analysis advanced options
Low value filter
Low-value filter allows you to specify criteria to exclude features that do not meet the requirements for the calculation. If there is a filter feature task performed in the upstream analysis, the default of this filter is set to None, otherwise, the default is Lowest average coverage is set to 1.
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Correlation across assays should be used to perform correlation analysis across different modalities (e.g. ATAC-Seq enriched regions vs. RNA-Seq expression) for multiomics data analysis. This option will only be available when multiple types of data are available in the project.
- Select the data node to be compared to the node that the task has been invoked from using the Select data node button
- Modify any parameters (Figure 4)
- Click Finish
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Correlation across assays analysis options
Correlation and similarity measures
Features within same chromosome: this option will restrict feature comparison to the chromosome location
All features in one data node vs all features in the other data node: this option will perform the comparison using all combinations without location constraint
Pearson: linear correlation:
Spearman: rank correlation:
Report correlation pairs
P-value: select a cut-off value for significance and only those pairs that meet the criteria will be reported
abs(Correlation coefficient): select a cutoff for reporting the absolute value of the correlation coefficient (represented by the symbol r) where a perfect relationship is 1 and no relationship is 0
Correlation across assays produces a Correlation pair list data node; double-click to open the list. table (Figure 5). The table can be sorted and filtered using the column titles.
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Click View correlation plot to open the correlation plot for each comparison. Scroll to the bottom of the table to download the full table report.
Additional assistance |
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