Entering edit mode
8 weeks ago
Stefano
•
0
I ran the heatmap2 tool on galaxy with the following settings:
Tool Parameters Input Parameter Value
Data transformation > Plot the data as it is;
Compute z-scores prior to clustering > none;
Scale data on the plot (after clustering) > Scale my data by row;
Enable data clustering > no;
Labeling columns and rows > Label my columns and rows;
Type of colormap to use > three; First color #0000ff Second color #ffffff Third color #ff0000;
Output format PDF;
As input file I used a simple gene expression matrix (each gene on a row, each column is a sample, 3 sample per condition, 2 conditions).
Can anyone tell me what the tool plots as output values to build the colors? Is it z-scores, LogFC or else? The color key indicates -1.5 to 1.5 as range. Thanks, appreciate any help!
As input file I used a simple gene expression matrix (each gene on a row, each column is a sample, 3 sample per condition, 2 conditions).
While someone may answer here, please post Galaxy related questions on their help forum as well: https://help.galaxyproject.org/