Entering edit mode
Hi guys, I am trying to run DE test with and would like to assign Age of Death (AOD) into the design function. My sampleinfo looks like this...(pretty simple really..)
Sample Treatment AOD
1 Low 98
2 Low 97
3 Low 87
4 Intermediate 80
8 Intermediate 77
9 Low 83
10 Low 92
11 Low 102
12 High 58
13 High 75
14 High 90
15 High 84
16 Intermediate 88
17 Control 82
18 Control 79
20 Control 87
24 Control 95
25 High 89
26 Intermediate 68
and I am trying to run
dds <- DESeqDataSetFromMatrix(countData = round(count),
colData = coldata,
design = ~ AOD+Treatment)
dds
and I get
Error in checkFullRank(modelMatrix) :
the model matrix is not full rank, so the model cannot be fit as specified.
One or more variables or interaction terms in the design formula are linear
combinations of the others and must be removed.
I read the vignette and checked if I had linear combinations, but I can't seem to find it... I have been going nuts over this for the past 2 hours can anyone help me please? Thanks!
Yes, I converted into factors by using
coldata$AOD <- as.factor(coldata$AOD)when I remove AOD and perform design = ~ Treatment, it works fine... What could cause this? Thanks!
Why did you make AOD into a factor? Do you understand what that does?
As suggested, you need to know better what you are trying to do. Converting AOD to factor means that each AOD become a caterogical variable and each AOD value is a unique category. If you convert it to factor (maybe you need it but I do not enough about know your experiment and statistical design), then absolutely your design matrix is not full rank because for each AOD value, a unique Treatment is possible. You need to better explain your experiment and your assumptions.