Why WGCNA modules don’t always agree with the dendrogram?

This post is about Dynamic Tree Cut, the method used, together with hierarchical clustering, to identify modules (clusters) in WGCNA. To put this post in context, in WGCNA, through several steps, one constructs a variable-variable similarity matrix which is then used for clustering. (The clustering similarity is usually the Topological Overlap Matrix, TOM, but it … Continue reading Why WGCNA modules don’t always agree with the dendrogram?

Removal of unwanted variation based on a subset of samples, with R code

Batch effects, technical variation and other sources of unwanted or spurious variation are ever-present in big data, especially so in high-throughput molecular (gene expression, proteomic or methylation) profiling. Fortunately, multiple methods exist for removing such variation that are suitable for various situations one may encounter. When a source of unwanted variation is known and can … Continue reading Removal of unwanted variation based on a subset of samples, with R code

Working with categorical variables

Most anyone working with any kind of data will have no trouble with binary outcomes (for example, case vs. control) and with relating them to continuous variables such as gene expression profiles. Indeed, the Student t-test or simple linear regression are some of the first topics encountered in data analysis. Categorical outcomes that encode more … Continue reading Working with categorical variables

Functional enrichment analysis via R package anRichment

At some point in most any analysis of high-throughput data one wants to study enrichment of a resulting set (or sets) of genes in predefined reference gene sets. Although there are many tools out there that let the user evaluate enrichment in standard reference sets such as GO and KEGG, there are relatively few that … Continue reading Functional enrichment analysis via R package anRichment

When can correlation network analysis be useful and when you are better off not using it

Weighted correlation analysis in general and WGCNA in particular can be applied to many problems and data sets, but certainly not to all. To set the terminology straight, recall that, in a correlation network, the each node represents a variable (feature), and links represent correlations, possibly transformed, among the variables. Although one could construct the … Continue reading When can correlation network analysis be useful and when you are better off not using it