Hi everybody,
I have been trying to use DESeq2 for analyzing RNA-seq data, and ran into a problem.
The conditions table looks like this:
When I specify the model for differential expression analysis as dds <- DESeqDataSetFromTximport(txi, samples, ~vpu+donor+virus), I get an error message:
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.
Same problem if the model is “vpu + virus” only.
I understand that this is because of collinearity among the variables but I am not sure how to resolve the issue.
Any help would be highly appreciated!
Thanks!
Chris
I have been trying to use DESeq2 for analyzing RNA-seq data, and ran into a problem.
The conditions table looks like this:
Code:
sample donor virus vpu DonorA1_01 A1 none mock DonorA1_02 A1 CH293 wt DonorA1_03 A1 CH293 stop DonorA1_04 A1 CH293 R50K DonorA1_05 A1 CH293 teth_count DonorA1_06 A1 CH077 wt DonorA1_07 A1 CH077 stop DonorA1_08 A1 CH077 R50K DonorA1_09 A1 CH077 teth_count DonorA1_10 A1 STC01 wt DonorA1_11 A1 STC01 stop DonorA1_12 A1 STC01 R50K DonorA1_13 A1 STC01 teth_count DonorX_01 X none mock DonorX_02 X CH293 wt DonorX_03 X CH293 stop DonorX_04 X CH293 R50K DonorX_05 X CH293 teth_count DonorX_06 X CH077 wt DonorX_07 X CH077 stop DonorX_08 X CH077 R50K DonorX_09 X CH077 teth_count DonorX_10 X STC01 wt DonorX_11 X STC01 stop DonorX_12 X STC01 R50K DonorX_13 X STC01 teth_count DonorY_01 Y none mock DonorY_02 Y CH293 wt DonorY_03 Y CH293 stop DonorY_04 Y CH293 R50K DonorY_05 Y CH293 teth_count DonorY_06 Y CH077 wt DonorY_07 Y CH077 stop DonorY_08 Y CH077 R50K DonorY_09 Y CH077 teth_count DonorY_10 Y STC01 wt DonorY_11 Y STC01 stop DonorY_12 Y STC01 R50K DonorY_13 Y STC01 teth_count DonorZ_01 Z none mock DonorZ_02 Z CH293 wt DonorZ_03 Z CH293 stop DonorZ_04 Z CH293 R50K DonorZ_05 Z CH293 teth_count DonorZ_06 Z CH077 wt DonorZ_07 Z CH077 stop DonorZ_08 Z CH077 R50K DonorZ_09 Z CH077 teth_count DonorZ_10 Z STC01 wt DonorZ_11 Z STC01 stop DonorZ_12 Z STC01 R50K DonorZ_13 Z STC01 teth_count
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.
Same problem if the model is “vpu + virus” only.
I understand that this is because of collinearity among the variables but I am not sure how to resolve the issue.
Any help would be highly appreciated!
Thanks!
Chris
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