Hello everyone, I had tried comparing two gene expression datasets in the .tsv file formats (reads quantified using Salmon) that were obtained from the RefineBio website. I was able to annotate the data using Galaxy using a GTF file from ENSEMBL, but when I tried using edgeR or limma, an error would occur. I was wondering if there is another way to compare datasets and build a volcano plot to show the differentially expressed genes between two samples.
RefineBio link to data: https://www.refine.bio/experiments/SRP117268/transcriptome-analysis-reveals-determinant-stages-controlling-human-embryonic-stem-cell-commitment-to-neuronal-cells
The expression files for each day (day0-22) are available. My goal is to compare day 0 with days 2, 4, and 6. I want to make volcano plots for each comparison and find the differentially expressed genes.
Thank you in advance !!