Hello

My name is Carlos. I am PhD student working on proteomic analysis from CSF. I am currently using the DESeq2 package in R to analyze the data, and wanted to ask if it is ok to use the negative binomial distribution on continuos data?

Is the correction factor in the DESeq2 package based on a ratio or on a multiplicative factor?

Kind regards,

CA

SWATH is MS1 quantitation in data independent (DIA) mode, i.e. not the kind of data one would typically view as count data.

If it's positive, but not counts or estimated counts of observations, I don't think count-based models are the right approach.

You might try limma-voom for finding differences (so scaling columns, log transforming, and estimating variance mean dependence from the data to inform the linear model)? Maybe Laurent can weigh in on whether that sounds reasonable.

limma is definitely a great option. I am not sure about the voom transformation.