Hello all, I am performing an analysis of a dataset for Th cells. We have performed differential gene expression of the microarray datasets and have obtained a list of differentially expressed genes from the analysis. Now as a next step I wanted to identify differentially expressed transcripts using the gene expression and protein dataset. For this we have tried a few approaches such as: performing differential expression analysis of the protein dataset using limma where we were unable to obtain the differentially expressed genes, we then combined both the data set using join function based on the common genes between both the datasets but was unable to identify top-up and top-down genes and also the volcano plot obtained was weird. Can anyone suggest an approach to deal with the gene and protein expression dataset where we can identify differentially expressed genes from the combined gene and protein expression datasets?
