Hello,
I have been using the online Express Analyst platform to analyze an RNAseq dataset from a mouse project (6 samples, 2 conditions). The same dataset and analysis settings that previously worked (a few months ago) now yield slightly different results, including fewer differentially expressed genes (DEGs) detected with identical filtering, adjusted p-value thresholds, and the DESeq2 test.
Additionally, I noticed issues in the pathway enrichment analysis outputs:
- In GSEA ridgeplots, the genes contributing to enriched pathways are now only displayed as Entrez IDs, making interpretation much harder.
- The CSV files for enriched pathways found with ORA ridgeplots no longer contain any gene details, reducing their usefulness.
- The interface reports different enriched pathways (with varying p-values) depending on whether they are accessed through the ridge plot, heatmap, or volcano plot menus.
- When attempting to generate a heatmap for an enriched pathway, double-clicking on the pathway name results in an error message: “No match found.”
Was there a significant update to the software since August 2024? If so, is there a way to access a previous version of Express Analyst? The earlier version provided more consistent results and fully functional pathway analysis tools, which were extremely helpful.
Any guidance on these issues would be greatly appreciated!
Best,
Jeanne