search for: rma2

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....

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="") >

...ns.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c mas5calls.c -o mas5calls.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c qnorm.c -o qnorm.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c rma2.c -o rma2.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c rma_background2.c -o rma_background2.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c rma_common.c -o rma_common.o gcc -shared -o affy.so chipbackground.o getall_locat...