# Compute biomarkers This task can be invoked from count matrix data node or clustering task report (*Statistics* > *Compute biomarkers*). It performs Student's t-tests on the selected attribute, comparing one subgroup at a time vs all the others combined. By default, the up-regulated genes are reported as biomarkers. * [Compute biomarker dialog](#compute-biomarkers-dialog) ## Compute biomarker dialog In the set-up dialog, select the attribute from the drop down list. The available attributes are categorical attributes which can be seen on the *Data* tab (i.e. project-level attributes) as well as and data node-specific annotation, e.g. graph-based clustering result (Figure 1). If the task is run on graph-based clustering output data node, the calculation is using upstream data node which contains feature counts – typically the input data node of PCA.

Figure 1. Compute biomarker dialog: selecting attribute

By default, the result outputs the features that are up-regulated by at least 1.5 fold change (in linear scale) for each subgroup comparing to the others. The result is displayed in a table with each column is a subgroup name, each row is a feature. Features are ranked by the ascending p-values within each sub-category. An example is shown in Figure 2. If a subgroup has fewer biomarkers than the others, the "extra" fields for that subgroup will be left blank.

Figure 3. Biomarkers table (example). Top 10 biomarkers for each cluster are shown. Download link provides the full results table

Figure 3. Biomarkers table (example). Top 10 biomarkers for each cluster are shown. Download link provides the full results table Furthermore, the **Download** link (upper-left corner of the table report) downloads a .txt file to the local computer (default file name: Biomarkers.txt), which contains the full report: all the genes with fold change > 1.5, with corresponding fold change and p-values. ## Additional Assistance If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis/compute-biomarkers.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.