My project focuses on differential gene induction between two stimuli. I want to see if genes are significantly induced across my entire time course and unfortunately I have only been able to detect a small amount when I know there are more.
I want to make sure that my code is executing the task properly. stimulus.final = stimulus- c1 or c2 stimulus.timepoint = timepoint in hours(0,1,2....) Code: DESEQ object:
dds_mat_final<- DESeqDataSetFromMatrix(data_mat_raw_final_matrix,colData=ColData,design= ~ 1 + stimulus.final+ stimulus.final.complete.timepoint) res_shrinkbl_local <-lfcShrink(res_local, coef="stimulus.final_c1_vs_c2",lfcThreshold=1) plotMA(res_shrinkbl_local, ylim=c(-3,3), main="Significant Genes Between c1 vs c2", xlab="Mean of Normalized counts between c1 vs c2", ylab="Log2 Fold Change Difference between c1 and c2")
Does using the coefficient "stimulus.final_c2_vs_c1" compare all of the stimuli across timepoints?