Hi all,

I use DESeq2 package for differential expression analysis ,where df is the the count data.

data1<-as.matrix(df)


##do differential expression
library(DESeq2)
dds <- DESeqDataSetFromMatrix(countData = data1,colData = pdata,design = ~ condition )
#reference is group2,so up means up in group1 and down means down in group1.


dds$condition <- relevel(dds$condition, "group2")
dds=DESeq(dds)
res <- results(dds)


I wanted to know what test is used in this by default "Wald test or LRT test  or no test " because I am not specifying anything in my command.

Thanks,

Rohan

Take a look at the ?DESeq2 help file and take note of the function signature:

DESeq(object, test = c("Wald", "LRT"), fitType = c("parametric", "local",
  "mean"), betaPrior, full = design(object), reduced, quiet = FALSE,
  minReplicatesForReplace = 7, modelMatrixType, parallel = FALSE,
  BPPARAM = bpparam())

Look at the test parameter. What you see here is a common idiom in R programming. When a function parameter takes an array like this c("Wald", "LRT"), it almost always implies that it expects the user to provide one of the values given in the vector of choices. This is usually checked with the a call to the match.arg function inside the function definition. When a user neglects to provide a value for the parameter, the first element on the "choice" vector is chosen, which in this case is "Wald".