3 Analysis

3.1 WGCNA

In the demo1, we used the gene expression table in different samples and the trait data of samples.

In the analysis parameters:

- Specify Bicor to calculate the correlation by selecting the option Bicor in the Aorrelation algorithms parameter;

- Ahoose a type of network by selecting the option Signed in the Network type parameter;

- Specify 30 to check by inputting 30 in the textarea of Specify maximum power to check parameter;

- Pick the top 2000 genes with the biggest difference between samples to analyse by inputting 2000 in the textarea of Only select top genes with maximum variances parameter;

- Remove outlier samples by selecting TRUE in the textarea of Remove outlier samples parameter;

- Specify -2.5 as the threshold for judging abnormal samples by inputting -2.5 in the textarea of Outlier sample detection threshold parameter;

- Specify 0.85 to define scale-free network by inputting 2 in the textarea of R square cut parameter;

- Detect the module whose size is lower than 25 by inputting 25 in the textarea of Minimum module size for module detection parameter;

- Specify 2 to split module by inputting 2 in the textarea of Deep split parameter;

- Set a random number to ensure that the result is repeatable by inputting 2020 in the Seed for random number generator parameter.

3.2 DE analysis (limma)

In the demo1, we used the raw reads count table in different samples and the metadata of samples.

In the analysis parameters:

  • Specify the type of input data by selecting the option Raw reads count in the Expression data type parameter;

  • Specify the column containing group information by selecting the option conditions in the Group parameter;

  • Remove outlier samples by selecting TRUE in the textarea of Detect and remove outlier samples parameter;

  • Do not detect and remove batch effect by selecting False in the textarea of Detect and remove outlier samples parameter;

  • The threshold is 1 and -1 of Log2 Fold change by inputting 1 in the textarea of Log2 Fold change parameter;

  • The threshold is 0.05 of FDR by inputting 0.05 in the textarea of False discovery rate parameter.