Model matrix not full rank
Entering edit mode
Last seen 2.7 years ago

Hi all, 

I would like to use DESeq2 to analyze a time series experiment of 6 time points each time point with 8 replicates. 3 time points are made in different time than the others, therefore they have a different batch.

My aim is to detect the genes varying over time in response to the treatment I'm doing.

While trying to include batch in the design its giving the error model matrix not full rank. When analyzing without including batch effect, I get a high number of significant genes and PCA plot is clustering samples based on batch not on time. Any help with this? 

Sample ID  time  batch 
Sham0.1 t0 b1
Sham0.2 t0 b1
Sham0.3 t0 b1
Sham0.4 t0 b1
Sham0.5 t0 b1
Sham0.6 t0 b1
Sham0.7 t0 b1
Sham0.8 t0 b1
Sham15I.1 t1 b2
Sham15I.2 t1 b2
Sham15I.3 t1 b2
Sham15I.4 t1 b2
Sham15I.5 t1 b2
Sham15I.6 t1 b2
Sham15I.7 t1 b2
Sham15I.8 t1 b2
Sham45.1 t2  b1
Sham45.2 t2  b1
Sham45.3 t2 b1
Sham45.4 t2 b1
Sham45.5 t2 b1
Sham45.6 t2 b1
Sham45.7 t2 b1
Sham45.8 t2 b1
Sham15IR.1 t3 b2
Sham15IR.2 t3 b2
Sham15IR.3 t3 b2
Sham15IR.4 t3 b2
Sham15IR.5 t3 b2
Sham15IR.6 t3 b2
Sham15IR.7 t3 b2
Sham15IR.8 t3 b2
Sham1hrIR.1 t4 b2
Sham1hrIR.2 t4 b2
Sham1hrIR.3 t4 b2
Sham1hrIR.4 t4 b2
Sham1hrIR.5 t4 b2
Sham1hrIR.6 t4 b2
Sham1hrIR.7 t4 b2
Sham1hrIR.8 t5 b2
Sham24.1 t5 b1
Sham24.2 t5 b1
Sham24.3 t5 b1
Sham24.4 t5 b1
Sham24.5 t5 b1
Sham24.6 t5 b1
Sham24.7 t5 b1
Sham24.8 t5 b1


design~ batch + time and for deseq function LRT test with reduced~batch


Thank you in advance for the help 

DESeq2 model matrix not full rank batch effect • 404 views
Entering edit mode
Last seen 6 hours ago
United States

It looks like batch and time are confounded. This is unfortunate, and not much can be done to remove batch, as it is mixed up with biological changes over time. Next time you should prepare the libraries using a block or randomized design.


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