Metabolink Documentation

= Data Format = The software is designed to handle a dynamic set of metadata fields, which are specific at the top of a tab delimited file. Here is a minimal example of a valid input file with two samples: Collection ID	1 Description Processing log Any field name	Value for Y1	Value for Y2 X	Y1	Y2 9.2	1.22	3.41 9.1	3.49	5.13 9.0	5.38	1.67

You can add additional information as you desire. Collection ID	1 Description Processing log Time	24	48 Dose	50 mg/kg	50 mg/kg X	Y1	Y2 9.2	1.22	3.41 9.1	3.49	5.13 9.0	5.38	1.67

You can create this document in Excel, but you must save it as a tab-delimited file. This file is referred to as a collection. Here is a template that you can modify to meet your needs:.

= Looking for differences between groups =

O-PLS

 * 1) Starting the program
 * In Windows you can start the program by clicking opls.exe, and on a Mac you may click on the opls application.
 * [[Image:metabolink_contents.png|800px]]
 * 1) A map of the interface
 * [[Image:metabolink_opls_map.png|800px]]
 * A - (Required) You can load your data by clicking this button. We currently support the tab delimited files described at the beginning of this document.
 * B - Once your data is loaded, you have the option of selecting two or more groups of data to create the model.
 * C - You also have the option of ignoring certain samples or groups of samples.
 * D - (Required) You can then specify how you would like the data grouped for visualization purposes. This may be different or identical to the model selection.
 * E - You also have the option of pairing your samples together.
 * F - This is where the scores plot of the model will be displayed.
 * G - The validation section allows you to specific k-fold cross-validation, leave-one-out cross-validation or bootstrapping.
 * H - You may also specify an alpha value for the significance of the model.
 * I - You may also select the number of permutations to use when validating with a randomization test.
 * J - (Required) Once you have selected your options, you can then run the model
 * K - Once the results are available, there are several different views available.
 * L - Here is where you can customize the plot that is created by clicking on the plot button.
 * M - Used to create a customized external plot
 * 1) Running O-PLS
 * After loading your data, selecting the appropriate options, and clicking run, you will be presented with a screen that looks like the following:
 * [[Image:metabolink_opls_results.png|800px]]