dseq2 results synergy contrast
1
0
Entering edit mode
steven wink ▴ 90
@steven-wink-5440
Last seen 4.8 years ago

Hi!

I am having some difficulty defining the correct contrast to test for synergy of two treatments A & B vs AB using the deseq2 results function. Treatment has 4 levels A, B, combined AB and reference level control.

When I set up contrasts e.g. ( AB - control ) - [(A - control) + (B - control)] I end up with AB - A - B + control! How can I get rid of the double counted control here? What am I missing? My design is ~ donor + condition + treatment + treatment:condition

Thanks in advance for your time.

deseq2 contrast synergy • 1.1k views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 1 hour ago
United States

Can you provide your colData, and more description of what you are looking to test for? You haven't described condition yet.

ADD COMMENT
0
Entering edit mode

Thanks for helping Michael, Condition has two levels. I want to test if the combined AB treatment is different from the additive A and B treatment (AB - A - B) within either conditions. First in the reference condition, later adding the interaction term to test within the hypoxia condition.

sample(rowname)         condition   treatment   donor
HSF1_hypoxia_A          hypoxia     A           HSF1
HSF1_hypoxia_AB         hypoxia     AB          HSF1
HSF1_hypoxia_B          hypoxia     B           HSF1
HSF1_hypoxia_control    hypoxia     control     HSF1
HSF1_normoxia_A         normoxia    A           HSF1
HSF1_normoxia_AB        normoxia    AB          HSF1
HSF1_normoxia_B         normoxia    B           HSF1
HSF1_normoxia_control   normoxia    control     HSF1
HSF2_hypoxia_A          hypoxia     A           HSF2
HSF2_hypoxia_AB         hypoxia     AB          HSF2
HSF2_hypoxia_B          hypoxia     B           HSF2
HSF2_hypoxia_control    hypoxia     control     HSF2
HSF2_normoxia_A         normoxia    A           HSF2
HSF2_normoxia_B         normoxia    B           HSF2
HSF2_normoxia_control   normoxia    control     HSF2
HSF3_hypoxia_A          hypoxia     A           HSF3
HSF3_hypoxia_AB         hypoxia     AB          HSF3
HSF3_hypoxia_B          hypoxia     B           HSF3
HSF3_hypoxia_control    hypoxia     control     HSF3
HSF3_normoxia_A         normoxia    A           HSF3
HSF3_normoxia_AB       normoxia     AB          HSF3
HSF3_normoxia_B         normoxia    B           HSF3
HSF3_normoxia_control   normoxia    control     HSF3
HSF4_hypoxia_A          hypoxia     A           HSF4
HSF4_hypoxia_AB         hypoxia     AB          HSF4
HSF4_hypoxia_B          hypoxia     B           HSF4
HSF4_hypoxia_control    hypoxia     control     HSF4
HSF4_normoxia_A         normoxia    A           HSF4
HSF4_normoxia_AB        normoxia    AB          HSF4
HSF4_normoxia_B         normoxia    B           HSF4
HSF4_normoxia_control   normoxia    control     HSF4
HSF5_hypoxia_A          hypoxia     A           HSF5
HSF5_hypoxia_AB         hypoxia     AB          HSF5
HSF5_hypoxia_B         hypoxia      B           HSF5
HSF5_hypoxia_control    hypoxia     control     HSF5
HSF5_normoxia_A         normoxia    A           HSF5
HSF5_normoxia_AB         normoxia   AB          HSF5
HSF5_normoxia_B         normoxia    B           HSF5
HSF5_normoxia_control   normoxia    control     HSF5
ADD REPLY
0
Entering edit mode

Easiest is to code this as colData with the columns: condition, A (ctrl/trt), and B (ctrl/trt).

Then your design is ~condition + A + B + condition:A + condition:B + A:B + condition:A:B

ADD REPLY
0
Entering edit mode

Not sure I fully understand, could you explain a bit more in detail? Did you note that I have 4 levels in my treatment column? (A, B, AB and control) As I read it now I would create extra dummy columns in colData consisting of ones and zeros, with column A having entries as ones for when treatment is control or treatment A, and column B having entries as ones for when treatment is control or B. On paper I would not be able to set up the correct contrast? I'd get this I think:
(A + control - B - AB) - (B + control - A - AB) so I still do not end up with A + B - AB.

ADD REPLY
0
Entering edit mode

The design I suggested will allow you to assess whether there is an interaction with A and B, and whether this is same or different across condition. As it’s a complex design, if you’re not certain about the terms and how to connect them to interpretations, I’d recommend you to collaborate with a local statistician.

ADD REPLY
0
Entering edit mode

I am trying to do a similar test for synergy between treatments with a somewhat simpler experimental design. I have data from 3 animals that were treated with hormone A, hormone B, or their combination. Each animal received each of the treatments, so my original model design includes blocking by individual: ~ Animal + Treatment.

I would like to test for synergy between treatments A and B. Can you please suggest a model design for this, as well as how to extract genes showing synergistic rather than additive effects using the results function?

colData:

sample            animal        treatment
con_rep1          1             control
con_rep2          2             control
cont_rep3         3             control
hormA_rep1        1             hormone A
hormA_rep2        2             hormone A
hormA_rep3        3             hormone A
hormB_rep1        1             hormone B
hormB_rep2        2             hormone B
hormB_rep3        3             hormone B
hormAB_rep1       1            hormone A + hormone B
hormAB_rep2       2            hormone A + hormone B
hormAB_rep3       3            hormone A + hormone B
ADD REPLY

Login before adding your answer.

Traffic: 609 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6