search for: qspline

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best combination. Thank you very much in advance. Roger Roger L. Vallejo, Ph.D. Computational Biologist & G...

Hi all, I have a data.frame e3. I use a function on it: n3 <- normalize.qspline(x = e3, samples = 0.07, na.rm = TRUE); The resulting data.frame has lost it's row-names and column names. This is the natural behaviour of the function I am calling, and I can't alter that at the moment. However, the data *is* in the correct order, as it was initially -- the names are ju...

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >