Introduction

Data once uploaded and filtered through the preceding tabs can be normalized and corrected for batch-effect. This guide particularly focuses on normalization of data for downstream analysis which can be achieved through various methods and options integrated together in a single interface. Generally, users can use one of the provided normalization methods integrated from other packages, or use transformation options to manually normalize/scale data. Additionally, these transformation options can be applied to normalized data as well depending upon the type of the transformation.

Available Transformation Options

Option Description
Log Transform Simple log base 2 transformation
log1p Natural log transformation and additionally adds 1 to remove zeros
Z-Score Standard z-score scaling
trim Trim values based on an upper and lower limits (can be applied with all of the above methods)

General Workflow

Workflow Guide

Normalization tab can be opened up by clicking on the Normalization & Batch Correction from the top menu and further selecting the Normalization sub-tab in the subsequent window as shown below.

The Normalization user-interface is divided into three parts, a) Normalization Options, b) Assay Options, and c) Available Assays.

a) Normalization Options

In the Normalization Options, users can select a method for normalization from Scater - CPM or one of the methods from Seurat i.e. LogNormalize, CLR (Centered Log Ratio), RC (Relative Counts) and SCTransform. Users can also set a manual Scaling Factor (numeric value multiplied by the data values) and specify the Assay Name for the new assay.

b) Assay Options

In addition to the normalization methods, manually implemented transformation methods can be used to perform different transformations on the data. These transformations include Log Transform, log1p and standard Z-score.

If trimming of an assay is required, ‘Trim Assay’ option can be enabled and lower/upper bound values can be set. The default value for upper and lower trim values is 10 and -10 respectively.

c) Available Assays

The currently available assays are listed in the ‘Available Assays’ window. Whenever a new assay is generated, the list is updated automatically.