A college of mine run an RNA-seq analysis using Galaxy a couple of years ago.
I used the same datasets to run a new analysis - and even though the list of genes generated was identical, I found discrepancies in the number of genes detected as significant (his dataset had more than a thousand significant hits, while mine had a handful).
When I looked closer to each dataset I discovered that the values were different in the two sets while p values and q values were recorded as ''0'' for the older dataset. I was wondering why this is the case.
|OLD DATASET:||chrom location:||Sample1:||Sample2:||status||value1||value2||log2 fold change||test-stat||p_value||q_value||significance|
|Npy||chr6:49822728-49829505||WT NaV1.8 DRG||V600E NaV1.8 DRG||OK||0.367901||692.945||10.8792||-12.1069||0||0||yes|