I have trying to perform DEseq2 analysis on my data. Some samples are sequenced in single end mode and some are in paired end mode. I would like to include this in the design when creating DESeq2 object.
Here is the example of `coldata` and what I was doing
sample subgroup type s1 G1 SE s2 G1 SE s3 G2 SE s4 G2 SE s5 G3 PE S6 G3 PE
For creating DESeq2 object
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ subgroup+type)
I'm getting the error related to 'Model matrix not full rank'. But the same design is working with the example data given in DESeq2 vignette. Any help would be greatly appreciated.