Experimental design

Modified on Tue, 15 Nov 2022 at 02:27 PM

The experimental design module of the is the second module you will encounter after data staging. In this module you will be able to edit metadata variables in the Algorithm box based on the users needs. 

Completing Experiment design is necessary for all downstream analyses. You can complete it once at the begining of your experiment or you can come back anytime to edit the metadata, like adding cluster names. 

1.  Creating a plot

1.1 Create plot

As a first step of the analysis, a plot must be created by clicking on the create plot icon. This will lead you to a section where the analysis of interest (in this case gene prioritisation analysis) can be selected.

The analysis can be effectively organised by assigning a name and description in the respective fields. Subsequently under the "choose algorithm to run your analysis", experimental design must be selected.

1.2 Selecting data

Next the input analysis can be selected into the track element under "choose track element". In the cell selection tab you can choose the observations to use as input. For more information see the section on Cell/sample selectionNote that subsetting at the pretreatment step is a "hard" subset meaning that excluded cells/samples at this step will not be present in the downstream steps.

1.3 Setting paramaters 

Once the appropriate parameters have been selected the analysis can be conducted. If no parameters appear simply continue onto running the analysis. 

1.4 Running the analysis

Once all the appropriate variables have been selected you can continue onto running the parameters. This can be achieved by clicking the run button on the top right corner

2. Interactive plot page: 

The interactive plot page presents you with various options where you can edit the metadata according to your preferences. The following aspects of your data can be edited using the tabs present on the right. Furthermore you will be able to export the table based on your preferred format. 

  • Edit variables: edit metadata vairables (i.e. columns). 
  • Edit values: edit metadata values. 
  • Add metadata: append new metadata columns from a file. 
  • Save settings: By clicking on this button the changes to the metadata will be saved. 

1.2.1. Experiment design algorithm settings - Edit variables

In this Edit variables tab you can edit metadata variables (i.e. metadata columns). You have the option to rename columns, change their order, merge columns together, make copies of columns and delete unwanted columns. This tab is highly interactive and we suggest viewing the tutorial video linked below. 

Metadata columns can be merged together by clicking on the Merge selected columns button. This can be useful, for example, when you have variables like Group (Normal, Tumour) and Batch (Batch 1, Batch 2, Batch 3). If you want to compare the Normal observations across batches, you would need to create a new metadata variable called GroupBatch (Normal_Batch 1, Normal_Batch 2, Normal_Batch 3, etc.). This is exactly what this option is for.

We suggest never deleting or modyfing original columns as to preserve trackability. If you want to modify an original column make a copy of it and then modify the copy. 

1.2.2. Experiment design algorithm settings - Edit values

In the Edit values tab you can edit the values stored in metadata columns. To do this click on the Recode values button to bring up the Recode column values modal.

In the Recode column values modal you can select which column's values you wish to edit and then edit the values in the "New value" column in the spreadsheet below. There is also an option to add or remove prefixes or suffixes. 

Changes made in this modal are saved only by clicking the Save metadata button in the Run tab!

By recoding values you can merge cells from different clusters together by simply giving them the same

1.2.3. Experiment design algorithm settings - Append metadata

In the Append metadata tab you can append the current metadata from metadata stored in a local folder. To do this click on the Append metadata file button to bring up the Append metadata modal.

Drag and drop the file which contains the new metadata columns you wish to the upload and append to the current metadata in the data upload area.

2. Saving changes

When all the input is provided click on the save settings button located on the top right. This will save all changes made in the metadata. Metadata can be edited again at anytime via the Edit metadata module. After running edit metadata module for the first time you should run the Data pretreatment module on your data. 

3. Video Tutorial

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