Question: Setting up the design for paired analysis
gravatar for candida.vaz
10 months ago by
candida.vaz40 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



limma edger paired design • 298 views
ADD COMMENTlink modified 9 months ago • written 10 months ago by candida.vaz40
Answer: Setting up the design for paired analysis
gravatar for James W. MacDonald
10 months ago by
United States
James W. MacDonald51k 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 10 months ago by James W. MacDonald51k

Thank you James for the suggestion,

ADD REPLYlink modified 9 months ago • written 9 months ago by candida.vaz40
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