Hello all,

I'm having trouble extracting and subsetting my dds for plotPCA. I only have one interested column called condition which I converted to factor along with the levels inside, c("Control", "Treatment1", "Treatment2", "Treatment3"). However, the code still prints out errors during the dds subset. For context, I generated my dds from DESeqDataSetFromTximport. I've succesfully plotted my global PCA, however I wanted to view different contrast groups to see the patterns, e.g. Treatment 1 vs Treatment 3 on PCA.

Though I get these error messages on colinearity and this one:

# Check if the column "condition" exists in colData
 if ("condition" %in% colnames(colData(dds))) { 
 colData(dds)$condition <- factor(colData(dds)$condition, levels = c("Control_Diet", "High_Fat_Diet", "Prophylactic", "Therapeutic"))
 } else {
 stop("Column 'condition' not found in colData(dds). Check your metadata.") }

> No warning message, so ran clear 
 # Define the levels of interest for subsetting
 levels_of_interest <- c("Prophylactic", "Therapeutic") 
>Ran clear
# Subset for levels of interest
 subset_dds <- dds[, colData(dds)$condition %in% levels_of_interest] 
>Ran clear
# Run DESeq2 analysis on the subset (optional)
subset_dds <- DESeq(subset_dds)
>Error in designAndArgChecker(object, betaPrior) : 
  full model matrix is less than full rank

Try droplevels on the condition:

dds$condition