I`m a bachelor student and for my bachelor thesis I need to build networks for gene expression analysis. I hardly get any support from anyone.
So I set up my DESeq2 dataset like this:
dds <- DESeqDataSetFromMatrix(countData = readcounts_bonobo,colData = coldata_Khrameeva, design = ~ brain_areal)
When I call on this I don't get any error.
This is what my coldata looks like:
Next I'm going to specify the factors for the comparison. I want to compare this 7 brain areas:
dds$brain_areal = factor(dds$brain_areal, levels = c("primary and secondary cortices","limbic and association cortices", "archicortex", "thalamus and hypothalamus", "white matter structures", "cerebellar gray matter", "striatum"))
This also works without any errors.
But when I want perform the differential expression analysis with:
dds = DESeq(dds)
I get this error:
Error in designAndArgChecker(object, betaPrior) : full model matrix is less than full rank
Is please anyone so kind to help me? I'm really desperate.