From anna.esteve at cnag.crg.eu Wed Jul 1 19:03:16 2020 From: anna.esteve at cnag.crg.eu (ANNA ESTEVE CODINA) Date: Wed, 1 Jul 2020 17:03:16 +0000 Subject: [NMF-user] cleaning dataset before running NMF Message-ID: Dear all, I am running the NMF R package to classify cancer samples but I am not sure if if it is advisable to clean my gene expression dataset from unwanted variation before. For example, I have covariates like sex, level of degradation, etc...that are counfounders. If so, how should I clean it? Regressing out these factors and working with the residuals? Are tools like SVA or ComBat appropriate? Thanks a lot for your feedback. Anna Esteve Codina, PhD Data Analyst Functional Genomics Unit Centre Nacional d'Ànalisi Genòmica CNAG-CRG Parc Científic de Barcelona -Torre I Baldiri Reixac, 4 08028 Barcelona email: anna.esteve at cnag.crg.eu web: http://www.cnag.crg.eu -------------- next part -------------- An HTML attachment was scrubbed... URL: