Hi, I am having the same problem, but don't understand Naomi's solution. What is the DEgene vector supposed to be if not my de.gene list? Thank you for your help. best wishes, Chris Christopher Gregg, PhD. Assistant Professor, Neurobiology and Anatomy Adjunct Professor, Human Genetics 323 Wintrobe Bldg 530 University of Utah, School of Medicine 20 North 1900 East, 401 MREB Salt Lake City, Utah 84132-3401 phone: (801) 581-8212 fax: (801) 585-9736 ------------------------------------ Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html<http: www="" .neuro.utah.edu="" labs="" gregg="" index.html=""> [[alternative HTML version deleted]]

The confusion for me seems to be from different variables in different explanations of the pipeline. My interpretation is the DEgene vector defined in the manual is the same as the gene.vector in the R script: gene.vector<-as.integer(assayed.genes %in% de.genes) Thus, one estimates the PWF with: pwf<-nullp(gene.vector, "mm9", "ensGene") This makes sense to me as this vector has the binary differential expression info. Am I performing the analysis as intended? Thank you again. Chris Christopher Gregg, PhD. Assistant Professor, Neurobiology and Anatomy Adjunct Professor, Human Genetics 323 Wintrobe Bldg 530 University of Utah, School of Medicine 20 North 1900 East, 401 MREB Salt Lake City, Utah 84132-3401 phone: (801) 581-8212 fax: (801) 585-9736 ------------------------------------ Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html