I have RNA-seq data of whole adipose tissue (adipocytes were not purified) and other clinical measurements.
When I run WGCNA analysis, I noticed that the modules that correlate with the features of interest are exclusively found in different cell types (in this case, it seems a positively correlated module are genes from immune cells, while negatively correlated modules are from adipocytes).
In that sense, I feel like the only solid conclusion I can get is that the proportion of these cell types change with the clinical feature of interest. This is an issue, as I am more interested in adipocytes.
My questions are:
1- Do you agree with this conclusion?
2- How do other researchers deal with data of whole tissue RNA-seq?
3- Is purifying the samples and redoing the RNA-sequencing the only alternative or is there a statistical solution? I assume rerunning the analysis with the currently available data using only genes expressed in adipocytes is not justifiable.