View Single Post
Old 03-14-2017, 06:10 AM   #10
Junior Member
Location: Lausanne

Join Date: Feb 2014
Posts: 5

I have been trying to use DESeq2 for analysing RNA-seq data in R and I have a small question about that.

So to start, the conditions table looks like this:

sample         donor    virus    vpu    sex
DonorA1_01    A1    none    mock    male
DonorA1_02    A1    CH293    wt    male
DonorA1_03    A1    CH293    stop    male
DonorA1_04    A1    CH293    R50K    male
DonorA1_05    A1    CH293    teth_count    male
DonorA1_06    A1    CH077    wt    male
DonorA1_07    A1    CH077    stop    male
DonorA1_08    A1    CH077    R50K    male
DonorA1_09    A1    CH077    teth_count    male
DonorA1_10    A1    STC01    wt    male
DonorA1_11    A1    STC01    stop    male
DonorA1_12    A1    STC01    R50K    male
DonorA1_13    A1    STC01    teth_count    male
DonorX_01    X    none    mock    female
DonorX_02    X    CH293    wt    female
DonorX_03    X    CH293    stop    female
DonorX_04    X    CH293    R50K    female
DonorX_05    X    CH293    teth_count    female
DonorX_06    X    CH077    wt    female
DonorX_07    X    CH077    stop    female
DonorX_08    X    CH077    R50K    female
DonorX_09    X    CH077    teth_count    female
DonorX_10    X    STC01    wt    female
DonorX_11    X    STC01    stop    female
DonorX_12    X    STC01    R50K    female
DonorX_13    X    STC01    teth_count    female
DonorY_01    Y    none    mock    male
DonorY_02    Y    CH293    wt    male
DonorY_03    Y    CH293    stop    male
DonorY_04    Y    CH293    R50K    male
DonorY_05    Y    CH293    teth_count    male
DonorY_06    Y    CH077    wt    male
DonorY_07    Y    CH077    stop    male
DonorY_08    Y    CH077    R50K    male
DonorY_09    Y    CH077    teth_count    male
DonorY_10    Y    STC01    wt    male
DonorY_11    Y    STC01    stop    male
DonorY_12    Y    STC01    R50K    male
DonorY_13    Y    STC01    teth_count    male
DonorZ_01    Z    none    mock    female
DonorZ_02    Z    CH293    wt    female
DonorZ_03    Z    CH293    stop    female
DonorZ_04    Z    CH293    R50K    female
DonorZ_05    Z    CH293    teth_count    female
DonorZ_06    Z    CH077    wt    female
DonorZ_07    Z    CH077    stop    female
DonorZ_08    Z    CH077    R50K    female
DonorZ_09    Z    CH077    teth_count    female
DonorZ_10    Z    STC01    wt    female
DonorZ_11    Z    STC01    stop    female
DonorZ_12    Z    STC01    R50K    female
DonorZ_13    Z    STC01    teth_count    female
Now 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” or "donor + sex".

I understand that this is because of collinearity among the variables but I am not sure how to resolve the issue as in my case all covariates are collinear to each other (and not just a pair of collinear variables).

Any help on this will be highly appreciated!

chammer is offline   Reply With Quote