path_values
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
path_values [2015/12/21 17:14] mhidalgo |
path_values [2020/04/03 20:18] (current) |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== Path values ====== | + | ====== Circuit values ====== |
| - | Here you will find descriptive information about the matrix of pathway values. | + | Here you will find descriptive information about the matrix of circuit/path values. |
| - | * **Path values**: You can download the matrix of path values by clicking on //Path values//. | + | * **Path values**: You can download the matrix of circuit values by clicking on //Path values//. |
| * **Heatmap**: A heatmap is a graphical representation of the values of a matrix. A not-supervised clustering is performed on the data per columns (samples). A good separation between the two colors of the upper bar of the heatmap indicates that the differences between the two groups are big enough to discriminate between them. | * **Heatmap**: A heatmap is a graphical representation of the values of a matrix. A not-supervised clustering is performed on the data per columns (samples). A good separation between the two colors of the upper bar of the heatmap indicates that the differences between the two groups are big enough to discriminate between them. | ||
| * **PCA**: A Principal Components Analysis is performed in order to see if the matrix contains information enough to separate between the two groups. | * **PCA**: A Principal Components Analysis is performed in order to see if the matrix contains information enough to separate between the two groups. | ||
| - | * **Path significance**: Ordered table of pathway significance. More significant pathways are displayed in the upper part of the table. For each pathway, the following information is shown: | + | * **Path significance**: Ordered table of circuit significance. More significant circuits are displayed in the upper part of the table. For each circuit, the following information is shown: |
| - | * **path/term**: Code identifying the path consisting in the name of the pathway to which it belongs, the initial node (if //Decompose paths// option was selected) and the effector (last) node of the path. | + | * **circuit/term**: Code identifying the circuit consisting in the name of the pathway to which it belongs and the effector (last) node of the path (//pathway Name : Effector//). |
| - | * **UP/DOWN**: Up when the path is up-regulated in the disease case, DOWN otherwise. | + | * **UP/DOWN**: Up when the circuit is up-regulated in the disease case, DOWN otherwise. |
| - | * **statistic**: Statistic of the of the statistic test. | + | * **statistic**: Statistic of the Wilcoxon test performed between conditions. |
| * **p.value**: P-value of the statistic test. | * **p.value**: P-value of the statistic test. | ||
| * **FDRp.value**: Adjusted p-value of the statistic test using the FDR method. | * **FDRp.value**: Adjusted p-value of the statistic test using the FDR method. | ||
| + | * **Fold Change**: is a measure describing how much the ** circuit activity** changes between conditions.[[https://en.wikipedia.org/wiki/Fold_change|reed more about Fold Change]] | ||
| + | * **logFC**: The logarithm to base 2 of calculated Fold change. | ||
path_values.1450718057.txt.gz · Last modified: 2020/04/03 20:18 (external edit)
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial 3.0 Unported
