zrl wrote: > Thank you Jim. I think you pretty much answered my questions. So, the > "var.cutoff" is actually the quantile of the IQRs calculated of all > the rows/genes. Do I understand this right? Yes. > > Thanks. > > Qiudao. > > On Tue, Feb 2, 2010 at 2:28 PM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> Hi Whomever, >> >> zrl wrote: >>> Dear list, >>> I am bit confused about the meaning of "var.cutoff" in function of >>> "nsFilter". Since we calculate the IQR of each gene, how could the >>> var.cutoff is a absolute value, 0.5. >>> When I read the help document, it says "Note that by default the >>> numerical-filter cutoff is interpreted as a quantile..." Does it mean >>> we really compare the IQR with region of quantile 0 to quantile 0.5? >>> Could someone help me clarify this? Thanks. >> I'm not sure what you are asking, so I'll just take a stab at it. >> >> The 'stock' setting of nsFilter takes each row of the data in your >> ExpressionSet and computes the IQR for that row. It then calculates what the >> median IQR is, and then removes the 50% of the data that have an IQR below >> that value. >> >> So if you change the var.cutoff to 0.2, you would remove the data with an >> IQR below the first quintile. Or if you changed var.cutoff to 0.75, you >> would remove the data with an IQR below the third quartile. >> >> Best, >> >> Jim >> >> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues