inst/helpfiles/tabPanel_drift.md

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

Trend line for aggregated values to indicate drifts/trends in data acquisition

This panel shows the sum- or median-aggregated values (specified in Select aggregation). The plot allows to display trends in data acquisition that originate e.g. from differences in instrument sensitivity. The panel allows to display aggregated values for

• raw (raw),
• normalized (normalized),
• normalized+batch corrected (batch corrected),
• normalized+batch corrected+transformed (transformed), and
• normalized+batch corrected+transformed+imputed (imputed)

assay values. The imputed data set can only be selected if there are missing values (NAs) in the raw data set. The different methods for normalization, transformation, batch correction, and imputation are specified in the side panel.

The smoothing is calculated from a selection of samples that are specified by the drop-down menus Select variable and Select level to highlight. The menu Select variable corresponds to the colnames in colData(se). Here, we can select for the higher-order variable, e.g. the sample type (containing for example Type_1, Type_2, ..., QC). The drop-down menu Select level to highlight will specify the actual selection from which the trend line will be calculated (e.g. Type_1, Type_2, ..., QC). Also, the menu will always include the level all, which will use all points to calculate the trend line. As an example, if we want to calculate the trend line of aggregated values of all samples belonging to the type QC, we select QC in the drop-down menu.

The panel allows for further customization after expanding the collapsed box. The data input is selected in the drop-down menu under Select data input. The smoothing method (either LOESS or linear model) is selected in the drop-down menu under Select smoothing method. The aggregation method is selected in the drop-down menu Select smoothing method.

With the drop-down menu Select categorical variable to order samples, the samples (x-axis) will be ordered alphanumerically according to the selected level (and the sample name).

tnaake/MatrixQCvis documentation built on June 20, 2024, 7:22 a.m.