Question: Setting up the design for paired analysis
gravatar for candida.vaz
7 weeks ago by
candida.vaz30 wrote:

Dear Bioconductor support team,

I have samples from two time points namely V1 and V4. The samples belong to two categories: Treatment and Placebo as follows:

005v1 Placebo 005v4 Placebo

008v1 Treatment 008v4 Treatment

The ID number 005 etc represent the same sample at two time points. At V1 time-point there is no treatment given, its just that the samples are assigned to be given a treatment (treatment) or not (placebo). At V4 time-point there would be difference in placebo and treatment sample.

Now, if the question is to identify the changes caused due to the treatment, how should I define the design? Should V1 time-point be taken into consideration or not, given that the treatment intervention was given only after the assignment of samples at V1.

It seems like a paired analysis, where the blocking factor is the IDs of the samples, but I'm not sure of setting up the design. Could someone give suggestions. Thanks in advance!


Candida Vaz



edger limma paired design • 114 views
ADD COMMENTlink modified 9 days ago • written 7 weeks ago by candida.vaz30
Answer: Setting up the design for paired analysis
gravatar for James W. MacDonald
7 weeks ago by
United States
James W. MacDonald49k wrote:

The edgeR User's Guide has a whole section (3.4) on Additive models and blocking, which should answer most if not all of your questions.

ADD COMMENTlink written 7 weeks ago by James W. MacDonald49k

Thank you James for the suggestion,

ADD REPLYlink modified 9 days ago • written 13 days ago by candida.vaz30
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