Differences

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--- parameters [2015/12/18 17:06] – created mhidalgo
+++ parameters [2021/01/07 17:02] (current) – krian
@@ Line 1: / Line 1: @@
-====== Parameters ======
+===== Experimental design =====
+This panel includes further parameters necessary to run a study.
+==== Paired ====
-**Decompose paths**: Check to consider subpathways with a unique input and a unique output in the analysis. When not selected the analysis is performed using subpathways with multiple inputs but a unique output (effector subpathways).
+Check to consider paired data in the analysis. When not selected the analysis is performed using unpaired parameter for the used statistical test-[[https://stat.ethz.ch/R-manual/R-devel/library/stats/html/wilcox.test.html|Wilcoxon]]-.\\ **Note:** The Experimental design file must be ordered.
+==== Unadjusted ====
-**Color nodes by differential expression**: Check to perform a gene differential expression and color each node depending on the adjusted p-value of the test.
+Check to don't use the FDR correction, this will select significant circuits depending on the p-value of the Wilcoxon test. (when not selected adjusted p-value will be used). [[https://en.wikipedia.org/wiki/False_discovery_rate|More about FDR...]]
+{{ ::parameters.png?nolink |}}
+==== Filter circuits ====
+Check to obtain the circuits that best differentiate your phenotype. This option is only available from //Prediction// tool.
+{{ ::filtercircuits.png?nolink |}}