If you want to track the differences across time between two groups in a single comparison, DiffBind
is not really set up to do that. You'd need to use one of the underlying analysis methods, like DESeq2
, directly. There are a number of threads discussing how to set up time series analyses in DESeq2
.
There are several things you can do in DiffBind
, provided you set up the metadata in a useful way.For example, if you set:
DBA_TISSUE
to be Precursor
, SubsetA
, or SubsetB
DBA_CONDITION
to be WT
or KO
(you can rename it Genotype
for display purposes)
DBA_TREATMENT
to be T00
, T06
, T18
, or T72
(you can rename it Timepoint
for display purposes)
DBA_REPLICATE
to be 1
, 2
, or 3
then you can compare:
- Overall differences between WT and KO, across all time points but independent of genotype:
dba.contrast(myDBA, group1=myDBA$masks$WT, group2=myDBA$masks$KO,
block=DBA_TISSUE)
- Overall differences between WT and KO, across either genotype but independent of time:
dba.contrast(myDBA, group1=myDBA$masks$WT, group2=myDBA$masks$KO,
block=DBA_TREATMENT)
- Differences between Genotypes A and B in WT, independent of time point:
dba.contrast(myDBA, group1=myDBA$masks$WT&myDBA$masks$SubsetA,
group2=myDBA$masks$WT&myDBA$masks$SubsetB,
block=DBA_TREATMENT)
- Differences between Genotypes A and B in WT at a specific timepoint:
dba.contrast(myDBA, group1=myDBA$masks$WT&myDBA$masks$SubsetA&myDBA$masks$T18,
group2=myDBA$masks$WT&myDBA$masks$SubsetB&myDBA$masks$T18)
- Differences between Precursor and each of the Genotypes in WT, independent of time point:
dba.contrast(myDBA, group1=myDBA$masks$WT&myDBA$masks$Precursor,
group2=myDBA$masks$WT&myDBA$masks$SubsetA,
block=DBA_TREATMENT)
dba.contrast(myDBA, group1=myDBA$masks$WT&myDBA$masks$Precursor,
group2=myDBA$masks$WT&myDBA$masks$SubsetB,
block=DBA_TREATMENT)
- And at a specific timepoint:
dba.contrast(myDBA, group1=myDBA$masks$WT&myDBA$masks$Precursor&
myDBA$masks$T18,
group2=myDBA$masks$WT&myDBA$masks$SubsetA&
myDBA$masks$T18)
Thank you very much, Rory, for your swift reply.
This is exactly what I want. Best wishes, Firas