Hi,
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
thanks,
Assa
Hi Assa. Are you trying to compare samples without replicates? This happens in this case.. Pvalues without replicates doesn't makes much sense anyway.
No I have for each condition either 3 or 4 replicates