On Sep 26, 2012, at 2:27 PM, David Winsemius wrote: > > On Sep 26, 2012, at 12:52 PM, JiangZhengyu wrote: >> >> Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 >> CG CG GG >> -- -- AC >> -- AC CC >> AC -- AC I tried to replace all the GG with a value 3. >> Gene[Gene=="GG"]<-3 It always give me: Warning in `[<-.factor`(`*tmp*`, >> thisvar, value = 3) : >> invalid factor level, NAs generated Does any know if there is anything wrong >> with my code? > > You are trying to replace a factor value with a level that it doesn't have. > Hence that particular very informative error message.
You probably could do this: Gene[] <- lapply(Gene, as.character) > Gene P1 P2 P3 1 CG CG GG 2 -- -- AC 3 -- AC CC 4 AC -- AC The use of the form `object[] <-` preserves the original dimensions. You would otherwise have needed to use data.frame() around the result. > Gene[Gene=="GG"] <- 3 > Gene P1 P2 P3 1 CG CG 3 2 -- -- AC 3 -- AC CC 4 AC -- AC > and provide commented, minimal, self-contained, reproducible code. Your code was not really self-contained and reproducible, but what I did was this: Gene <- read.table(text="P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC", header=TRUE) read.table will by default create factors when the input column contains character values unless you use stringsAsFactors=FALSE. -- David Winsemius, MD Alameda, CA, USA ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
