Deseq generating warning "the model matrix is not full rank"

Question

[MAPK2]

I am trying to run this analysis, but it generates the warning shown below. Can someone please help me figure out the issue?

ddset = DESeqDataSetFromMatrix(
    countData = counts.matrix,
    colData = properties2, 
    design = ~Group + (1 | Cell_type)
)

Error in checkFullRank(modelMatrix) : 
  the model matrix is not full rank, so the model cannot be fit as specified.
  Levels or combinations of levels without any samples have resulted in
  column(s) of zeros in the model matrix.

  Please read the vignette section 'Model matrix not full rank':

  vignette('DESeq2')
In addition: Warning message:
In Ops.factor(1, Cell_type) : ‘|’ not meaningful for factors

properties2

Sample_ID   Group   Cell_type
XX          No       XX_CF
XX_DOX      Yes      XX_CF
YY1         No       YY1_KO_CF
YY1_DOX     Yes      YY1_KO_CF
YY2         No       YY2_KO_CF
YY2_DOX     Yes      YY2_KO_CF
XY2         No       XY2_KO_CF
XY2_DOX     Yes      XY2_KO_CF

[ATpoint]

In plain english, which question do you want to answer and what do you think does the design mean?

[bioruffo]

Group and Cell_type are factors of how many levels? Check str(properties2) ... Did you start with a metadata file where e.g. there were other Cell_type levels? If so, Cell_type might still be a factor with 3+ levels. You can try using e.g. properties2$Cell_type <- droplevels(properties2$Cell_type) .