Question: Help with matrix design
0
gravatar for ivan.vechetti
4 months 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 • 108 views
ADD COMMENTlink modified 4 months ago by Gordon Smyth38k • written 4 months ago by ivan.vechetti0
Answer: Help with matrix design
1
gravatar for Gordon Smyth
4 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k 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 4 months ago • written 4 months ago by Gordon Smyth38k

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

ADD REPLYlink written 4 months ago by ivan.vechetti0
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