After I have performed Cuffdiff in Galaxy on my two RNA-Seq data of different treatment conditions, I loaded my SQLite data into RStudio to see the differentially expressed genes. However, after I command; "gene_diff_data <- diffData(genes(cuff_data))" I don't see any data available in R. The only available info in R is "0 obs. in 11 variables". What could be the reason for this? Where have I done wrong? My galaxy run progressed pretty smoothly.
Thank you! Efraim