[BioC] goseq problem

[Christopher T Gregg]

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
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Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html