How to extract a set from your experimental data for analysis in Analytics?

Created by Arie Baak, Modified on Wed, 3 May, 2023 at 7:32 AM by Arie Baak

OVERVIEW

Before you can analyze your experimental data in Analytics, you need to create an input set. Two types of input sets for Analytics can be created: simple set (containing a column of concepts) and effect set (containing a second column with values).

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.

edit_complex_set_in_Sets

3. The complex set window opens up. The options (clear buttons) for creating simple and effect set are on the top of the page.

A) Extract a set of concepts from the complex set: click the [Create simple set] button to open the pop-up window.

Select the column in your set you want to save as a simple set in the [Column name] dropdown box.
Click one of the options in the [Type] section that depicts the type of concepts in the selected column.
Click one of the options in the [Taxonomy] section in which the concepts in selected column belongs. Select from the dropdown list if the species is not shown. This is required if the concepts in the selected column are genes or proteins. Otherwise, this setting will be be ignored.
Click the [Analyze] button. The concepts will now be recognized by the Euretos platform and linked to the knowledge base. For a large set, this step might take a long time. When there are ambiguous concepts, you need to choose the ones you want (more details in this article).
Click the [Save as simple set] button to save the set. Once all the concepts are recognized, a [Create simple set] pop-up window appears for you to change the name, description, and tag of the created simple set.
The recently saved simple set will be at the top of the list in the [Sets] menu.

B) Extract a set of concepts along with a single associated measurement data from the complex set: click the [Create simple set] button to open the pop-up window.

Select the column in your set you want to save as an effect set in the [Column name] dropdown box.
Click one of the options in the [Type] section that depicts the type of concepts in the selected column.
Click one of the options in the [Taxonomy] section in which the concepts in selected column belongs. Select from the dropdown list if the species is not shown. This is required if the concepts in the selected column are genes or proteins. Otherwise, this setting will be ignored.
Select the column from your set you want to save as the values of the effect set in the [Measure] dropdown box.
Click the [Analyze] button. The concepts will now be recognized by the Euretos platform and linked to the knowledge base. For a large set, this step might take a long time. When there are ambiguous concepts, you need to choose the ones you want (more details in this article).
Click the [Save as effect set] button to save the set. Once all the concepts are recognized, a [Create effect set] pop-up window appears for you to change the name, description, and tag of the created effect set.
The recently saved effect set will be at the top of the list in the [Sets] menu.

If the selected column from your set you want to save as simple or effect set contains duplicated entries, you will be prompted with the following error message: to perform aggregation:

Error_when_creating_simple_or_effect_set

In this case, follow Step 3B from this article to aggregate the data set and then proceed wit the simple set or effect set extraction.

Possible Next Step

Understand the type of analyses in [Analytics] you can perform on sets
Perform gene set enrichment analyses on the sets extracted from your experimental data

How to extract a set from your experimental data for analysis in Analytics?

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