I have some RNA-seq analysis that I want to do and determine differential gene expression with respect to several different phenotypic characteristics. For some of these, we can group the data (i.e. control, treatment), but we also want to determine differential gene expression with respect to several continuous variable such as fat mass and age.
Is there a way to determine differential gene expression in R without having to divide the samples into distinct groups, and to look at differential expression with respect to increasing age for example?
The edgeR user guide has in depth description of GLM analyses (page 15) suitable for many types of analyses such as correcting for gender (factor) while looking for genes that correlate with age (continuous). I understand that DESeq provides more or less the same functionality too. NicoBxl's suggestion of stratifying individuals into groups is an excellent suggestion.