I know if there is one control and one treatment group it is pretty straight forward to interpret log 2 fold change. But, I have time course experiment. I have infected cells with viruses and I harvested cells at different time points: o hr, 6 hour, 12 hr and 24 hour. Here o hr is my non-infected control. What is the best way to show log 2 fold change for each gene in this type of time course experiment. I ultimate aim to find highly expressed genes at different time points.
You should analyze your data with a proper statistical framework such as
DESeq2. The vignette offers a section about time series experiments plus there are plenty of questions about it on the Bioconductor support forum, just use google to find them. It might be worth looking at the shrinkage function in
DESeq2 to get more appropriate log2 fold changes for lowly-expressed genes. I hope you have replicates. If not, please use google and the search function for posts on RNA-seq analysis without replicates. THere is a lot of material on this available both here on Biostars as well as on the BioC support forum and the web.