Question: Help with matrix design
0
gravatar for ivan.vechetti
29 days ago by
ivan.vechetti0 wrote:

Hello all,

I'm currently facing 2 independent variables to try to input on Limma to do DE analysis, but I haven't been able to. I have muscle samples with 9 different metals implanted (n=2 per metal) and a time-course (1, 3, 6 and 12 months). Here I use one of the metals as a control (since it should be inert), and I want to be able to tell the differences among metals in a specific period of time as well as see the changes with time. Is there a way to design a matrix for this experiment?

Thanks in advance

limma • 72 views
ADD COMMENTlink modified 28 days ago by Gordon Smyth37k • written 29 days ago by ivan.vechetti0
Answer: Help with matrix design
1
gravatar for Gordon Smyth
28 days ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

The experiment you describe is similar in structure to that in your previous post

https://support.bioconductor.org/p/121009/

and you can use the same method as before. Previous you had 2 genotypes x 4 time points, now you have 9 metals x 4 time points, but that doesn't cause any complication. Exactly the same approach will work as before.

The fact that one of the metals is a control has no effect on the design matrix, it only affects which comparisons (contrasts) are of interest to you.

ADD COMMENTlink modified 28 days ago • written 28 days ago by Gordon Smyth37k

I thought as much. But I only wanted to make sure. Thanks again

ADD REPLYlink written 28 days ago by ivan.vechetti0
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: 269 users visited in the last hour