Hi, the experiment that I conducted consists of a control and 4 different concentrations of chemical treatments (5 replicates per treatments) under two different exposure time (12 hours and 48 hours). As I was interested to compare the expression profile between the two time points, I found out there is a batch effect caused by sequencing both time points at different batches from my PCA plots: the 12hours group has separated entirely from the 48 hours group, even for my two control groups they were also far far away from each other.

Can I therefore treat the exposure time as a batch effect in my DESeq design model? What disadvantage would there be the batch is exactly same as the exposure time? I couldn't find similar posts or suggestion as I had searched in google. Here I would like to treat the chemical concentration as a linear model

dds <- DESeqDataSetFromMatrix(counts, metadata, design = ~time + chemical.con )

DESeq(dds)

resultsNames(dds)
[1] "Intercept" "time"      "chemical.con"

Something doesn't look right here, seems like I couldn't compare the expression profiles between 8 days and 4 days, any advice?

Thank you very much