To specify biological replicates, you must add a study factor called the Biological Replicate Factor. You can add only one biological replicate factor; if one already exists, the application makes the Biological Replicate Factor menu item unavailable.
The application displays a biological replicate factor with a specific Replicate icon.
When the study contains a replicate factor, the Grouping and Quantification page in the study shows which biological replicates are contained in the generated sample groups. Within each sample group, the application groups samples belonging to the same biological replicate and highlights them with a yellow box showing the replicate name. The following figure shows samples grouped by the time course time point. There are several sample groups, each a different time point in the time course of this experiment. The replicates are grouped together in yellow boxes containing the replicate name appended to the front of each quan channel.
The Generated Ratios pane on the Grouping and Quantification page shows which ratios you created.
In nested experiments, where each sample group contains the same biological replicates, the pane also shows that sample group ratios are created using replicate ratios.
When there are biological replicates in the study, the Precursor Ions Quantifier node or the Reporter Ions Quantifier node creates columns showing abundances of biological replicates for proteins and peptide groups. It calculates abundances and ratios as described earlier. It calculates abundances for biological replicates using sample abundances, which you can normalize and scale, as appropriate.
The node can calculate p-values for non-nested experiments. If the ANOVA (Individual Proteins) p-value method is selected, it can calculate p-values for nested experiments only when each sample group includes two biological replicates. For the ANOVA (Background-Based) method, p-values can be calculated even when there is only a single biological replicate.