Hi I'm wondering if someone can help confirm if my contrast is correct. What want is to compare one set of analysis to another. Like a venn diagram. Circle one would be Exp A and Exp B would be another circle, so now I want to know what the different between these two experiments are.

Lets call one exp A and the exp B so now essentially I want to know the difference of the difference. Can someone help confirm my contrast below to see if I'm doing this correctly?

I think its correct, `cmp = (A_exp-A_control) - ( B_exp - B_control)`

however why I'm concern is that when I ran pathway analysis, this analysis yield the same pathways that was present in both (A_exp-A_control) and ( B_exp - B_control) when done alone ( below contrast would be expA and expB, respectively)? How would this be possible?

thank you in advance.

```
input <- 'id group
S1 A_control
S2 A_control
S3 A_control
S4 A_exp
S5 A_exp
S6 A_exp
S7 B_control
S8 B_control
S9 B_control
S10 B_exp
S11 B_exp
S12 B_exp
'
df = read.table ( text=input, header=T)
group = df$group
design <- model.matrix(~0 + group )
colnames ( design) = gsub ( 'group',"",colnames(design))
contrast.matrix <- makeContrasts(
,cmp = (A_exp-A_control) - ( B_exp - B_control)
,expA = (A_exp-A_control) # these would be simple comparison of exps in isolation.
, expB = ( B_exp - B_control)
,levels=design
)
```

thanks for the confirmation. I'm still baffle why similar pathways from hypegeometric test are showing up on all three test including the interaction.

Might also be informative to do

all this time I did not thought to use this. VennDiagram was super useful but the the table even more useful to do some fast comparisons.

`data.frame ( decideTests(fit.r, lfc=1) )`

then I can filter any combination I needed; very cool thank you I learned a couple of useful things today.