Diego Espinoza

icon company University of Pennsylvania, Perelman School of Medicine icon location Philadelphia, PA icon location MD-PhD Student

Results 2 comments of Diego Espinoza

Different results between different runts

Even with 10000 permutations, the GSEA function returns different results on each run. reproducible example below: ``` data(geneList, package="DOSE") m_t2g % dplyr::select(gs_name, entrez_gene) GSEA(geneList, TERM2GENE = m_t2g, minGSSize = 120,...

Pandas version of as_matrix is deprecated

I've been able to get around this by locally going into `algo.py` and changing line 214 from `expression_matrix = expression_data.as_matrix()` to `expression_matrix = eexpression_data.as_numpy()`