Hallo,

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.

Thank you.

The model matrix not full rank error also comes with a pointer to a section of the vignette. Have you taken a look there? This particular case is discussed. 

Here is a link:

http://master.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#model-matrix-not-full-rank