Question: Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
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gravatar for Rob Buurstede
3 months ago by
Rob Buurstede0 wrote:

Hi all,

I'm struggling with the question of how to properly analyze the RNA-seq data I'm currently working on and your insights are very welcome. As a second question, we're interested in looking at the effect of treatment over time, so a design with time and treatment is the obvious option - with a total of 6 groups.

However, as the experiment was not designed with this in mind, the data consist of 5 groups (n=5/group). For each treatment there is a group at 1.5h and 3h, but the t=0 time point is represented by a single naive group of animals.

My question is whether or not I can analyze the data together (including the t=0 for both groups in some way), or if I should analyze the 1.5h en 3h time points for each treatment apart from the t=0 time point and check separately what the expression does per treatment over time.

Biologically, I expect both groups at t=0 to be similar, but of course there would still be an amount of variation between the groups. Another suggestion I received is to split the t=0 group in two so you do have six groups for the analysis, but this will results in very small groups.

Curious to hear your thoughts on this.

Thank you very much,

Rob

ADD COMMENTlink modified 3 months ago by Michael Love25k • written 3 months ago by Rob Buurstede0
Answer: Analysis strategy - possible to use naive control group as t=0 for two treatment
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald51k wrote:

This support site is intended to help people with technical questions about Bioconductor software, not help people with statistical advice. I would in general recommend getting local help from a statistician with whom you can have a collaborative relationship rather than depending on free advice from random internet people, but if that's your thing, you might try at biostars or stackoverflow.

ADD COMMENTlink written 3 months ago by James W. MacDonald51k
Answer: Analysis strategy - possible to use naive control group as t=0 for two treatment
0
gravatar for Michael Love
3 months ago by
Michael Love25k
United States
Michael Love25k wrote:

I'd echo James' point that you may do well to discuss the statistical approach with a local collaborator.

For DESeq2 you're probably just best off having a factor group with levels for all the 5 groups. You can then do pairwise comparisons. Unlike the time course example in the vignette, you can't for example, remove the baseline differences (t=0) for the treated samples because those samples don't exist.

ADD COMMENTlink written 3 months ago by Michael Love25k

Dear Michael,

Thank you for your response. I am indeed discussing the issue with a local statistician, but I was also curious to hear if there where option within Deseq2 which I did not know about that might suit this experimental setup.

Based on your advice I will stick to the pairwise comparison I initially started with.

Thank you,

Rob

ADD REPLYlink written 3 months ago by Rob Buurstede0
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