Question: Creating the correct design
0
gravatar for skamboj
13 days 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 • 65 views
ADD COMMENTlink modified 12 days ago by Michael Love24k • written 13 days ago by skamboj0
Answer: Creating the correct design
0
gravatar for swbarnes2
13 days ago by
swbarnes2220
swbarnes2220 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 13 days ago • written 13 days ago by swbarnes2220
Answer: Creating the correct design
0
gravatar for Michael Love
12 days ago by
Michael Love24k
United States
Michael Love24k 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 12 days ago by Michael Love24k
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