Hello all,
I want to use a GLM in EdgeR on raw fragment counts generated from cuffdiff. I have 4 groups (A,B,C,D) with 4 biological replicates each. I want to determine if there is a significant difference between the fold change between A/B and the fold change C/D. So I want to look at significant differences of significant differences. I am thinking of using the following command in EdgeR:
> my.contrast <- makeContrasts((A/B)-(C/D), levels=design)
> lrt <- glmLRT(fit, contrast=my.contrast)
Can anyone give me a sanity check on this?
I want to use a GLM in EdgeR on raw fragment counts generated from cuffdiff. I have 4 groups (A,B,C,D) with 4 biological replicates each. I want to determine if there is a significant difference between the fold change between A/B and the fold change C/D. So I want to look at significant differences of significant differences. I am thinking of using the following command in EdgeR:
> my.contrast <- makeContrasts((A/B)-(C/D), levels=design)
> lrt <- glmLRT(fit, contrast=my.contrast)
Can anyone give me a sanity check on this?