I would like to ask about design matrix in GLM model in edgeR. I have group
of transgenic down regulate gene. We have 3 lines of transgnics per down
regulate gene which different level (event) of down regulate gene and in
each line we have 3 replicate. This means we have 9 sample per 1 gene
downregulate. This experiment also have double down regulate (2 genes down
regulate at the same time). We would like to find gene that change when we
down regulate target gene. I create event1-9 to seperate the transgenic
event. I try design matrix as show below and can't perform GLM. It show "

Error in solve.default(R, t(beta)) :
  system is computationally singular: reciprocal condition number =
3.13057e-17

If i change the design metric to column1-3 (effect of mean,geneA and
geneB), this new design matric work well. How can i desing matric that
account for effect of transgnic event?


  mean geneA geneB event1 event2 event3 event4 event5 event6 event7 event8
event9
wt 1 0 0 0 0 0 0 0 0 0 0 0
wt 1 0 0 0 0 0 0 0 0 0 0 0
wt 1 0 0 0 0 0 0 0 0 0 0 0
down_a 1 1 0 1 0 0 0 0 0 0 0 0
down_a 1 1 0 1 0 0 0 0 0 0 0 0
down_a 1 1 0 1 0 0 0 0 0 0 0 0
down_a 1 1 0 0 1 0 0 0 0 0 0 0
down_a 1 1 0 0 1 0 0 0 0 0 0 0
down_a 1 1 0 0 1 0 0 0 0 0 0 0
down_a 1 1 0 0 0 1 0 0 0 0 0 0
down_a 1 1 0 0 0 1 0 0 0 0 0 0
down_a 1 1 0 0 0 1 0 0 0 0 0 0
down_b 1 0 1 0 0 0 1 0 0 0 0 0
down_b 1 0 1 0 0 0 1 0 0 0 0 0
down_b 1 0 1 0 0 0 1 0 0 0 0 0
down_b 1 0 1 0 0 0 0 1 0 0 0 0
down_b 1 0 1 0 0 0 0 1 0 0 0 0
down_b 1 0 1 0 0 0 0 1 0 0 0 0
down_b 1 0 1 0 0 0 0 0 1 0 0 0
down_b 1 0 1 0 0 0 0 0 1 0 0 0
down_b 1 0 1 0 0 0 0 0 1 0 0 0
down_ab 1 1 1 0 0 0 0 0 0 1 0 0
down_ab 1 1 1 0 0 0 0 0 0 1 0 0
down_ab 1 1 1 0 0 0 0 0 0 1 0 0
down_ab 1 1 1 0 0 0 0 0 0 0 1 0
down_ab 1 1 1 0 0 0 0 0 0 0 1 0
down_ab 1 1 1 0 0 0 0 0 0 0 1 0
down_ab 1 1 1 0 0 0 0 0 0 0 0 1
down_ab 1 1 1 0 0 0 0 0 0 0 0 1
down_ab 1 1 1 0 0 0 0 0 0 0 0 1

Thank you very much
Sermsawat T.

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