Hi all,

I'm trying to remove the "age" batch effect of my samples. It is basically a column, where each individual sample has an different age with 2 decimal digits. I defined the column as a factor and then used it in the "design" of DESeq2.

I get the following error:

Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed.

I have read the vignette and did not come up with a solution. I assume it has to do with the fact that "it doesn't know" how to treat the ages as groups. Meaning, what are ages which are in proximity.

Please help me find a solution to this one.

Best

Don't define it as a factor. Either use it as a continuous covariate or discretize into buckets (this is actually in the FAQ). You can consult a statistician to understand why a linear model with a coefficient for each observation cannot be used to perform inference.