I used following command to filter out 3 groups (NC, BF, CF) out of 5 groups while remaining two groups are "AF" and "DF".
design_NCaF <- filter(design, Groups1!="NC",Groups1!="BF",Groups1!="CF")
However, at following command
NCaF <- DESeqDataSetFromMatrix(data_max_woNCaF, colData=design_NCaF, design = ~Groups1 + Patient)
It gives me following error message
factor levels were dropped which had no samples 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. Is it because of remaining two groups have different sample size (AF=6 and DF=3) ?