I have two questions about EdgeR pipeline. I am dealing with no replicate situation and have two conditions to check the differential expression. I am trying to apply GLM model for the analysis. I am bit confused about the design.
I am running following commands to setup design -
design <- model.matrix(~group, data=cds$samples) design (Intercept) groupRest Rest 1 1 Bcyt 1 0 attr(,"assign")  0 1 attr(,"contrasts") attr(,"contrasts")$group  "contr.treatment"
Is this design right for the experiment? how to set up to proper design for the experiment?
2) with this setup I carried out glm analysis. but the end I am not able to export my results in to the table. I run following command for exporting data -
After this I am getting following error -
Error in data.frame(coefficients = c(-0.55319099962599, -0.597451121359484, : arguments imply differing number of rows: 25299, 1, 2
Please help me to solve this problem
Thank you in advance
Thank you Aaron!
Hi Aaron I have another que. What will happen if I setup design without intercept?
Then you'll have to use
glmLRTin order to compare the two samples.