Hello!
I have an inquiry about what package works best for my dataset since I find it a bit complex to understand.
I have a proteomics dataset; fish were exposed to 2 different drug treatments and a control, and each fish had its mucus sampled before exposure, 15 days after exposure, and 30 days after exposure (making it a repeated measures design).
Effectively, there is control for the treatment (0mg, 5mg, 10mg), and for the time (Day 0, Day 15 and Day 30).
Additionally, the proteomics data I have is in the form of peak intensities- where the rows are protein names, columns are the samples and the cells contain peak intensity values
What package works best with such a proteomics dataset, since a lot of them are designed mainly for transcriptomics data?
Any suggestions and explanations are welcome, since I would like to learn and apply this further!
Thank you:)
Thank you!
I was also reading on limma-voom, they suggest not using it on spectral count data, but is it okay to use on peak intensity data?
I didn't say limma-voom. Just limma.
You may need to use limma-trend if there is a relationship between the mean and variance of your intensity data, but that's up to you.