DESeq2 "not full rank" with design design ~Gender+ Age
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sofia • 0
@725046bd
Last seen 23 hours ago
Canada

Hello, I am using DESeq2 to perform differential expression analysis. I have forty samples, gender and age are the variables in my colData. However, when I ran the code, it gave me the error that " the model matrix is not full rank". Initially, I thought it is because there's a sample that has a missing value in colData, so I removed that sample from dds and colData, but the error still exists. I read the vignette section of "Model Matrix not Full Rank", and I think the problem I am having probably matches the "levels without samples" condition (Like there's no certain age in the Female or Male group), but I am not really sure. Could you please help me check my design and see if I need to remove the columns of 0 manually from the model matrix?

dds= DESeqDataSetFromMatrix(countData = cts,
colData = colData,
design = ~ Sex + Age
)

as.data.frame(colData)

Age    Sex
<fctr>.   <fctr>
sample_01   17      F
sample_02   16.1    M
sample_03   10.4    M
sample_04   15.3    F
sample_05   14.5    F
sample_06   18.1    M
sample_07   14      F
sample_08   15.6    F
sample_09   11.1    F
sample_10   9.5     -

DESeq DESeq2 • 78 views
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Entering edit mode
swbarnes2 ▴ 780
@swbarnes2-14086
Last seen 14 hours ago
San Diego

You don't want age to be a factor. Input your coldata with stringsasfactors = false, then make sex a factor manually.

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