I'm trying to analysis a time-series RNA-seq data using DESeq2, I have 15 time points, 2 conditions, and 2 biological repeat.
I perform LRT test first and the full model is ~batch + condition + time + condition:time, while the reduce model is ~batch + condition + time. All variances are recognized as factor. I choose the threshold fdr < 0.01 and get ~5000 different expressed genes.
Then I want to map these different expressed genes at each time point and perform wald test of these different expressed genes at each time point. I use the threshold fdr < 0.01 and | log2FoldChange | > 1 but only ~2000 genes could be mapped in the time points. Then I loose the delimitation and use the threshold only fdr < 0.01, there are ~3000 genes could be mappped in specific time points.
I want to make sure whether my method of process time-series data is right. If so, what is the biological meaning of these genes could not mapped in specific time points.
Thanks a lot!!