I'm working on a mouse data set, where the mice were exposed to different treatments (HP, DR). In the experiment we have 9 conditions with 3 (or 4) samples per condition. I have one "zero" control and two controls after pre-conditioning of the mice. I also have two time points were RNASeq data was prepared (4h and 24h). we did both RNASeq and miRNA-Seq.
We are running multiple comparisons and all looks well, except one comparisonin the miRNASeq data set. In this comparison I get an adjusted p-value of 1 for all the genes. The comparison is between the zero control and one of the controls after pre-conditioning. In the RNASeq data we get good results with quite a few significant genes under the threshold adj. p-value.
I know it can't be directly compared, but it is a comparison of the workflow which I would like to point to.
I would like to know, what can be the explanation for an adjusted p-value of 1 in all genes, when the p-value and log2FC looks quite normal.
my DESeq2 version is 1.8.1