How to filter and edit an experimental data set after uploading?

Created by Arie Baak, Modified on Wed, 3 May, 2023 at 7:05 AM by Arie Baak

OVERVIEW

Now that you have uploaded your experimental data into platform, you might want to filter the data based on specific criteria. This article outlines the steps for filtering as well as editing your uploaded data set.

STEPS

Note	A user action, such as click or enter, is italicized. A visible item on the platform, such as a [link] or a [button], is in square brackets. A link to another article or external source is underlined.

1. Find the uploaded complex set you want to edit in the [Sets] menu.

Note	Headers located above the list of sets allows you to sort and filter based on the title of the set, the tags associated with the set or the type of set. The set type should be labeled as [Complex].

2. Click the [pencil] icon or the set name to open the complex set.

!	Important: The set you want to upload must be saved in csv format and contain multiple columns of data including at least one with measurement data.

2. Click the [+ Create] button on the [Sets] page: this opens up the [Add set] page where you can upload the set.

3. The complex set window opens up. The options (blue buttons) for filtering, removing duplicates, and editing the complex set are at the top of the page.

complex_set_screen_filter_edit_config

A) Filter the complex set based on a specified cutoff: click the [Add filter] button to define one or more filters for the set. The [Filter Set] pop-up window appears.

Select the column that the filter will be applied in the [Column name] dropdown box.
Select whether the concepts that meet the criteria should be excluded [Y
es] or included [No] from the result list in the [Excluded] dropdown box.
Select the type of operation for the filter which includes: = (equal to); > (greater than); >= (greater than or equal to); <(less than); or <= (less than or equal to) in the [Operation] dropdown box.
Enter a value for the filter in the [Value] fill-in box.
Click the [Add filter] button to save the
filter specifications.
Click the [Add filter] button on the top of the complex set page and repeat the above steps to add multiple filters. Example: keep genes with either 'log2FC' greater than 1.5 or 'log2FC' less than -1.5 (shown below):
Click the [Apply Filters] button to apply the filter(s). You can view the saved filter(s) above the data table. The set is now applied to the set. You can also apply filter in sequential step to filter the set: add filter, apply filter, add filter, apply filter and so forth. Example: those genes with absolute 'log2FC' greater than or equal to 1.5, keep those with 'pvalue' less than 0.05 (shown below):

B) Remove duplicated concepts containing different measurement data from a complex set: click the [Aggregate Set] button. The [Filter Set] pop-up window appears.

Select the column of concepts that will be aggregated in the [Identifier Column] dropdown box.
Select the column of values on which the aggregation method will be applied in the [Aggregation Column] dropdown dox.
Select the type of method to be applied to the selection in the [Aggregation Column]: Min (takes the minim value); Max (takes the maximum values); Median (takes median value); or Mean (calculates the average value).
Click the [Apply Aggregation] button to apply the aggregation to the set.
Click the [Aggregate Set] button on the top of the complex set page and repeat the above steps to apply multiple aggregations.
Example: For a complex set of differentially expressed genes, if you select 'gene' as the identifier and aggregate by ‘log2FC’ and ‘Min’, all duplicate genes will be removed by keeping the one with the lowest value for 'log2FC'.

4. Click [Restore Complex Set] button to reset any applied filters and aggregation if you want to restore it back to the original set at any time.

5. Click the [Save Complex Set] button to save the modified complex set. This brings you back to the [Sets] main page.

Note

The most recently modified set will appear as the top one in the list. Notice that the modified set contains the word 'Modified' as part of the set name. Edit the name and description of the set to reflect the changes:

Click the file name or the [pencil] icon to open the modified complex set.
Click the [Config Set] button on the top of of the page. The [Edit complex set] window appears where changes to name, description, tag, and column contents of the set can be made.

config_set_screen

Click the [Submit] button to apply the changes.
Click [Yes] in the pop-up window when asked [Make a set copy with new name?]
Click the [Sets] menu to return to the [Sets] main page to view the edited set containing the new name and description.
Click the [recycle] bin next to the copy with the old set name to delete it.

Possible Next Step

Create an input set for analysis in [Analytics]

How to filter and edit an experimental data set after uploading?

OVERVIEW

STEPS

A user action, such as click or enter, is italicized.

A visible item on the platform, such as a [link] or a [button], is in square brackets.

A link to another article or external source is underlined.

Headers located above the list of sets allows you to sort and filter based on the title of the set, the tags associated with the set or the type of set. The set type should be labeled as [Complex].

Possible Next Step