Entering edit mode
9 months ago
MAPK2
▴
50
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
In plain english, which question do you want to answer and what do you think does the design mean?
Group
andCell_type
are factors of how many levels? Checkstr(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)
.