I want to correct my dataset for batch instead of including batch in the formula. The reason is that it seems that my data is not coming for certain sub-analysis from all batches and therefore I get a "Full Rank"-Error. The Bioinformatics Core therefore suggested to run Combat (not Limma) to correct for the batch.
Now I am struggling a bit how to do it.. I have my data - colData and cts which I want to run after with
dds <- DESeqDataSetFromMatrix(countData = cts, colData = colData, design = ~SEX + DIAGNOSIS
How do I run combat with my colData and cts? I need to build a matrix?! But I need colData and cts seperate after to build the dds object?
I am a bit confused right now...
Thank you for any hint!