Question: Switching RNAseq count data to explanatory variable?
0
gravatar for jrager
14 days ago by
jrager0
jrager0 wrote:

I am trying to figure out if there is a way to modify the design formula such that countData are used as the "effect" / explanatory variable, and another outcome is used as the dependent variable, while adjusting for covariates. So, I'm trying to switch:

countData ~ covariate1 + covariate2 + outcome

to

outcome ~ covariate1 + covariate2 + countData

Is this an option? Or should this kind of question represent something you could still ask about using the first formula listed?

Thank you for your time.

deseq2 • 93 views
ADD COMMENTlink modified 14 days ago by Michael Love25k • written 14 days ago by jrager0
Answer: Switching RNAseq count data to explanatory variable?
0
gravatar for Michael Love
14 days ago by
Michael Love25k
United States
Michael Love25k wrote:

Short answer is, this isn’t something you can do with DESeq().

Both designs are a little bit strange because the outcome is not a fixed effect (like, control, treatment or batch).

How many samples do you have? What is the context here?

ADD COMMENTlink written 14 days ago by Michael Love25k

Thank you for the response. This is a more general question for several ongoing projects - we have a large sample count (~500) from human tissue. We are trying to evaluate relationships between gene expression signatures and various epidemiology-based outcomes. For instance, does the expression level of a gene(s) associate with an outcome that occurs later-in-life.

I cannot provide further details through public forum - is that enough?

ADD REPLYlink modified 14 days ago • written 14 days ago by jrager0

I wouldn’t usually put an observation like the counts from an RNA-seq experiment (normalized or not) as an independent variable in a design. You may want to have a model that incorporates a latent factor driving the counts and another outcome.

ADD REPLYlink written 14 days ago by Michael Love25k

Great- this confirms our thoughts. Thank you for the feedback!

ADD REPLYlink written 13 days ago by jrager0

Great- this confirms our thoughts. Thank you for the feedback!

ADD REPLYlink written 13 days ago by jrager0
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