I have a question re filtering for low variance prior to WGCNA. I have got RNASeq data, pre-filtered for low counts and transformed with DESeq2 vst. I was wondering if you could help me select from the two methods below the one that is more correct for my data.
filter <- function(x)(IQR(x, na.rm=T)>0.25) filtered_genes <- genefilter(df,filter) df_filtered<-df[filtered_genes,]
data$variance = apply(data, 1, var) data = data[data$variance >= quantile(data$variance, c(0.25)), ] data$variance <- NULL
Thank you very much for your help!