Three types of files need to be uploaded.
Note: please download templates for these files and check that the column names of your files match the template's column names and sheet name matches the template's sheet name.
Previewing files in the main panel:
Choose the focal raw file in the selection panel for the outlier removal process.
Users can set Robust Z-score[1] and screen using pre-screen thresholds if required.
After clicking the Remove outliers button, outliers will be removed and plots will be displayed on the main panel. Plots can be viewed with the selected measurement (e.g. diameter, area, etc.).
Users can manually override cell results by selecting cells. The result of a selected cell will be toggled after applying the manual override (e.g. an outlier cell will be converted to a non-outlier cell).
The report of the selected file can be downloaded by clicking the download button.
A table of raw files will be shown on the main panel after uploading raw data files. The second column (column name: Processed) shows whether the file has gone through the outlier removal. The rest of the columns show the configuration (e.g. robust z score value) used in outlier removal. Downloaded outlier removal reports can also be uploaded and used in merging.
The merged file is only available when selected raw files have been processed.
Plots of the merged data can be created and viewed. The app supports bar plots, point plots, dot plots and box plots.
Plots can be added to the report of files and downloaded.
[1] Malo, N., Hanley, J., Cerquozzi, S., Pelletier, J. and Nadon, R., 2006. Statistical practice in high-throughput screening data analysis. Nature Biotechnology, 24(2), pp.167-175.