How to resolve this Error in checkFullRank(modelMatrix) in DESeq2 ?

Question

[Raheleh]

Hi, I have two factors in the design formula in DESeq2

dds <- DESeqDataSetFromMatrix(as.matrix(count.3), colData=colData, design = ~ Genotype + Batch)

but got an error, I can't find any reason for this error. I searched and it seems everything is ok.

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.

Can anyone help me to solve it? Thanks!

This is my colData:

          Genotype     Batch
X2111111_S39    A     4
X2121111_S40    A     4
X2131111_S41    A     4
X2141111_S42    A     4
X2151111_S43    A     4
DFR18201_S21    A     12
RJR18171109_S6  AK    5
RJR18171109_S7  AK    5
RJR18171109_S8  AK    5
DFR182011_S2    AK    12
DFR182011_S4    AK    12
DFR182011_S5    AK    12
RJR1817111_S16  BP    5
RJR18180418_S1  BP    17
RJR18180418_S2  BP    17
RJR18180418_S3  BP    17
KPRJR1817_S20   BPN   3
KPRJR1817_S21   BPN   3
KPRJR1817_S22   BPN   3
RJR18171_S15    BPN   5
RJR18171_S17    BPN   5
RJR18180418_S4  BPN   17
RJR18180418_S5  BPN   17
AKNR18200_S1    KPN   8
AKNR18200_S3    KPN   8
AKNR18200_S7    KPN   8
VKPNKF_RQQ_S6   KPN   10
VKPNKF_RQQ_S9   KPN   10
VKPNKF_RQQ_S7   KPN   10
VKPNKF_RQQ_S8   KPN   10
NMR18200_S11    KPN   14
NMR18200_S12    KPN   14
NMR18200_S13    KPN   14

[andrew.j.skelton73]

Have you got batch set as numeric or factor?

[Raheleh]

Thanks, as factor

Genotype <- factor(meta$Abbreviation)
Batch <- factor(meta$Batch)
colData <- data.frame(Genotype, Batch)
rownames(colData) <- rownames(meta)
dds <- DESeqDataSetFromMatrix(as.matrix(count.3), colData=colData, design = ~ Genotype + Batch)

[andrew.j.skelton73]

Is that the full table in your OP? Seems that KPN is the problem, as batches 8, 10, 14 are not across any other genotypes. I suspect that if you fit the model, this coefficient would not be estimable