Once these two datasets are in R, DetectiV prepares them for analysis using the prepare.data function. This function joins the array data to the probe information data based on a unique ID. The researcher may choose to subtract local background if appropriate. The default at this stage is to average over replicate probes, again based on a unique ID. This will result in a single value for each unique probe for each array. The data will have one or more columns of extra information from the annotation file, and these columns will be used to group the data for further analysis.