Question: Creating the correct design
0
gravatar for skamboj
3 months ago by
skamboj0
skamboj0 wrote:

I've been having some trouble with getting my pipeline to execute what I want. Below is my ColData, and what I would like to look at is the following. First I would like to look at the main effect of treatment. I tried Design = Clone + Treatment and did a contrast of VPA vs Unt, but the results were way higher then they should've been, so something isn't right.

Then, I would like to look at the interaction effect, which I believe can be done with Design= Disease + Treatment, but I am not sure if I am executing things correctly, and I don't believe my resultsName(dds)- is showing me what I would like...but basically would like to look at SMS-VPA vs SMS-Unt, Cont-VPA vs Con-Unt etc etc

Any advice or help with be greatly appreciated

    Clone Disease Treatment Age
AT.1    A1  SMS   VPA       Y
AT.2    A2  SMS   VPA       Y
AT.3    A3  SMS   VPA       Y
AU.1    A1  SMS   Unt       Y
AU.2    A2  SMS   Unt       Y
AU.3    A3  SMS   Unt       Y
OT.1    O1  Con   VPA       Y
OT.2    O2  Con   VPA       O
OT.3    O3  Con   VPA       O
OU.1    O1  Con   Unt       Y
OU.2    O2  Con   Unt       O
OU.3    O3  Con   Unt       O

deseq2 • 120 views
ADD COMMENTlink modified 3 months ago by Michael Love25k • written 3 months ago by skamboj0
Answer: Creating the correct design
0
gravatar for swbarnes2
3 months ago by
swbarnes2330
swbarnes2330 wrote:

Have you done PCA on your samples to see how they look compared to each other?

To do a simple comparison of one subset of samples to another subset of samples, make a new column in ColData that is the disease concatenated to the treatment, and make that your design.

ADD COMMENTlink modified 3 months ago • written 3 months ago by swbarnes2330
Answer: Creating the correct design
0
gravatar for Michael Love
3 months ago by
Michael Love25k
United States
Michael Love25k wrote:

Take a look at the vignette section on interactions first.

Secondly, if you want to do some exploration, use plotCounts on the top genes to understand why they are identified as DE.

ADD COMMENTlink written 3 months ago by Michael Love25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 213 users visited in the last hour