the model matrix is not full rank : This is a classic question which a biologist face without clear understanding of the model design Saw this answer biostar. Tried to make my metadata as such but still the
&quot;Error in checkFullRank(modelMatrix) : &quot;

This is my coldata
dput(coldata)
structure(list(Group = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 
6L, 6L, 6L, 6L), .Label = c(&quot;HSC&quot;, &quot;Blast&quot;, &quot;CMP&quot;, &quot;GMP&quot;, &quot;LSC&quot;, 
&quot;Mono&quot;), class = &quot;factor&quot;), Mutation = structure(c(10L, 4L, 3L, 
5L, 2L, 3L, 9L, 11L, 1L, 1L, 7L, 7L, 10L, 7L, 8L, 2L, 10L, 10L, 
10L, 10L, 2L, 2L, 7L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 2L, 2L, 5L, 2L, 
9L, 1L, 1L, 8L, 6L, 6L, 6L, 6L, 6L, 6L), .Label = c(&quot;DNMT3A-R882H&quot;, 
&quot;FLT3-ITD&quot;, &quot;IDH2-R140Q&quot;, &quot;KRAS-G13D&quot;, &quot;MAU2-Q98H&quot;, &quot;No&quot;, &quot;NPM1-L287ins(TCTG)&quot;, 
&quot;NRAS-G13D&quot;, &quot;STAG2-R614&quot;, &quot;TET2-E1357&quot;, &quot;TET2-R550&quot;), class = &quot;factor&quot;), 
    Satus = structure(c(2L, 5L, 4L, 6L, 3L, 4L, 9L, 10L, 1L, 
    1L, 7L, 7L, 2L, 7L, 8L, 3L, 2L, 2L, 2L, 2L, 3L, 3L, 7L, 16L, 
    16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 
    16L, 16L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 12L, 12L, 13L, 
    12L, 9L, 11L, 11L, 14L, 15L, 15L, 15L, 15L, 15L, 15L), .Label = c(&quot;Blast-DNMT3A-R882H&quot;, 
    &quot;Blast-E1357&quot;, &quot;Blast-FLT-ITD&quot;, &quot;Blast-IDH2-R140Q&quot;, &quot;Blast-KRAS-G13D&quot;, 
    &quot;Blast-MAU2-Q98H&quot;, &quot;Blast-NPM1-L287ins(TCTG)&quot;, &quot;Blast-NRAS-G13D&quot;, 
    &quot;Blast-STAG2-R614&quot;, &quot;Blast-TET2-R550&quot;, &quot;LSC-FLT-DNMT3A-R882H&quot;, 
    &quot;LSC-FLT-ITD&quot;, &quot;LSC-MAU2-Q98H&quot;, &quot;LSC-NRAS-G13D&quot;, &quot;Mature-Normal&quot;, 
    &quot;Progenitor-Normal&quot;, &quot;Stem-Normal&quot;), class = &quot;factor&quot;)), row.names = c(&quot;Blast1&quot;, 
&quot;Blast10&quot;, &quot;Blast11&quot;, &quot;Blast12&quot;, &quot;Blast13&quot;, &quot;Blast14&quot;, &quot;Blast15&quot;, 
&quot;Blast16&quot;, &quot;Blast17&quot;, &quot;Blast18&quot;, &quot;Blast19&quot;, &quot;Blast20&quot;, &quot;Blast2&quot;, 
&quot;Blast21&quot;, &quot;Blast22&quot;, &quot;Blast23&quot;, &quot;Blast3&quot;, &quot;Blast4&quot;, &quot;Blast5&quot;, 
&quot;Blast6&quot;, &quot;Blast7&quot;, &quot;Blast8&quot;, &quot;Blast9&quot;, &quot;CMP1&quot;, &quot;CMP2&quot;, &quot;CMP3&quot;, 
&quot;CMP4&quot;, &quot;CMP5&quot;, &quot;CMP6&quot;, &quot;CMP7&quot;, &quot;CMP8&quot;, &quot;GMP1&quot;, &quot;GMP2&quot;, &quot;GMP3&quot;, 
&quot;GMP4&quot;, &quot;GMP5&quot;, &quot;GMP6&quot;, &quot;GMP7&quot;, &quot;HSC1&quot;, &quot;HSC2&quot;, &quot;HSC3&quot;, &quot;HSC4&quot;, 
&quot;HSC5&quot;, &quot;HSC6&quot;, &quot;HSC7&quot;, &quot;LSC1&quot;, &quot;LSC2&quot;, &quot;LSC3&quot;, &quot;LSC4&quot;, &quot;LSC5&quot;, 
&quot;LSC6&quot;, &quot;LSC7&quot;, &quot;LSC8&quot;, &quot;Mono1&quot;, &quot;Mono2&quot;, &quot;Mono3&quot;, &quot;Mono4&quot;, &quot;Mono5&quot;, 
&quot;Mono6&quot;), class = &quot;data.frame&quot;)

dds &lt;- DESeqDataSetFromMatrix(countData=df2, colData=coldata, design= ~ Group + Mutation)

This is the design I'm trying to incorporate. What i get is my design is nested in one of the column by looking at numerous example.
What i would like to do is I'm trying to run a LRT test on this dataset which works fine if i give &quot;Group&quot; as my design and then i run this
dds_lrt &lt;- DESeq(dds, test=&quot;LRT&quot;, reduced = ~ 1)

which gives me diffrenitaly expressed across multiple groups. Now there are two question

Is it possible to include interaction such as in my case Group+Mutation and do the lrt test?
Or the above is conceptually wrong to do ?
&gt; table(doldat$Group, coldat$Mutation)
       
        DNMT3A-R882H FLT3-ITD IDH2-R140Q KRAS-G13D MAU2-Q98H No NPM1-L287ins(TCTG) NRAS-G13D STAG2-R614 TET2-E1357 TET2-R550
  HSC              0        0          0         0         0  7                  0         0          0          0         0
  Blast            2        4          2         1         1  0                  4         1          1          6         1
  CMP              0        0          0         0         0  8                  0         0          0          0         0
  GMP              0        0          0         0         0  7                  0         0          0          0         0
  LSC              2        3          0         0         1  0                  0         1          1          0         0
  Mono             0        0          0         0         0  6                  0         0          0          0         0

Look at this table, you see by eye how some mutations are nested with Group. If you want to include it then you will need to subset the experiment into multiple separate runs, depending on the question you want to answer.