Differences

This shows you the differences between two versions of the page.

--- design_data [2015/12/21 09:42] – mhidalgo
+++ design_data [2021/01/07 16:56] (current) – [**Two-group comparison**] krian
@@ Line 3: / Line 3: @@
 ===== Design data panel =====
-The design data panel allows you to choose the kind of experiment you want to perform. You can choose between three kinds of experimental design:
+The design data panel allows you to choose the kind of experiment you want to perform. You can choose between two kinds of experimental design:
-  * **Two group comparison**: The comparison is performed between the two groups described in the experimental design file. The experimental design file must include two columns: the first one with the names of the samples, the second one with the class to which each sample belongs.
+==== Two-group comparison ====
+The comparison is performed between the two groups described in the experimental design file.\\ The experimental design file must include **two columns**: the first one with the names of the samples, the second one with the class to which each sample belongs.
+{{ ::designdatacomp.png?nolink |}}
+If the experimental design file contains more than two classes then you have to select the appropriate class for each condition.\\ **Note:** the condition 2 will be taken as a reference condition.
+{{ ::morethantwoclass.png?nolink |}}
-  * **Correlation with continuous variable**: A correlation is performed between the values of each path along the samples and the continuous variable introduced. The experimental design file must include two columns: the first one with the names of the samples, the second one with the value of the variable for each one of the samples.
+==== Correlation with continuous variable ====
-  * **Mutation effect**: The comparison is performed between the expression matrix without considering the mutations, and the expression matrix resulting from integrating the information about the mutations. No experimental design file is needed, but the use of a VCF file is mandatory. This option is only available from the //Differential signaling// tool.
+A correlation is performed between the values of each effector circuit along the samples and the continuous variable introduced.\\ The experimental design file must include **two columns**: the first one with the names of the samples, the second one with the value of the variable for each one of the samples.
+{{ ::designdatacorr.png?nolink |}}