Hi,
I get very different results when I perform Deseq2 by choosing 3 factor levels under 1 FACTOR vs performing Deseq2 individually 3 times to compare the three factor levels to each other So, I am unable to say which is the correct result.
DeSeq2 Run1
FACTOR 1: TREATMENT
Factorlevel1: conditionA
Factorlevel 2:conditionB
Factorlevel 3: conditionC
(I also checked the box that says :Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)
This one generates 3 result files comaring A vs B, B vs C and A vs C. However, these results are very different to that obtained when I run DeSeq2 individually as follows.
DeSeq2Run2
FACTOR 1: TREATMENT
Factorlevel1: conditionA
Factorlevel 2:conditionB
DeSeq2Run3
FACTOR 1: TREATMENT
Factorlevel1: conditionA
Factorlevel 2:conditionC
DeSeq2Run4
FACTOR 1: TREATMENT
Factorlevel1: conditionB
Factorlevel 2:conditionC
Can someone please help.
Many thanks,
GG