I am performing differential expression on gene expression between different time points- time point 0 vs. time points 0.5, 1 and 3.
For a specific gene, I have the following expression profile (this is normalized reads):
It seems in the plot like there is a significant difference between time points 0 and 1. Actually, this is a gene which I know is induced in this paradigm from many past experiments. However, DESeq does not find the comparison significant:
baseMean log2FoldChange lfcSE stat pvalue padj GeneX 1230.466 1.277551 1.164463 1.097116 0.2725906 0.8389563
The individual values of time point 0 are:
tp0.1 tp0.2 tp0.3
1622.129 1260.146 1831.165
and for 1:
tp1.1 tp1.2 tp1.3
2878.453 4137.590 4406.023
If I perform a simple t-test on the two time points, I get p-value = 0.0304.
My question is- what might be the reason that this comparison is coming up as insignificant in the DESeq analysis? Thanks a lot!