Question: How to generate proteomics reaction norms via generalised linear models?
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gravatar for niklasjoshua.ebner
9 days ago by
Switzerland/Basel/Department of Environmental Sciences
niklasjoshua.ebner0 wrote:

Hi everyone,

I would like to recreate reaction norms of protein abundance data similar to this study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540970/

Essentially, a GLM with negative-binomial distribution was applied to gene expression data (count data). They treated the treatment (temperature) as a continuous variable instead of doing pairwise comparisons.

I have a protein abundance matrix (~1200 rows, 18 columns) with three treatments (6 biological replicates per treatment) with the treatments being different temperatures (10, 15 and 20 °C).

Now my question is how can I apply a glm to this data in R and sort by proteins that i) increase with increasing temperature, ii) decrease with increasing temperature, iii) show a U- or a Bell-shape and group the proteins together belonging to one of the above "reaction norms"?

I hope someone can help me out here.

Best

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