Hu, Ying (NIH/NCI) wrote: > I have two data sets: > File1.txt: > Name id1 id2 id3 ... > N1 0 1 0 ... > N2 0 1 1 ... > N3 1 1 -1 ... > ... > > File2.txt: > Group id1 id2 id3 ... > G1 1.22 1.34 2.44 ... > G2 2.33 2.56 2.56 ... > G3 1.56 1.99 1.46 ... > ... > I like to do: > x1<-c(0,1,0,...) > y1<-c(1.22,1.34, 2.44, ...) > z1<-data.frame(x,y) > summary(glm(y1~x1,data=z1) > > But I do the same thing by inputting the data sets from the two files > e <- read.table("file1.txt", header=TRUE,row.names=1) > g <- read.table("file2.txt", header=TRUE,row.names=1) > e1<-exp[1,] > g1<-geno[1,] > d1<-data.frame(g, e) > summary(glm(e1 ~ g1, data=d1)) > > the error message is > Error in model.frame(formula, rownames, variables, varnames, extras, > extranames, : > invalid variable type > Execution halted > > Thanks in advance, > > Ying
You have several inconsistencies in your example, so it will be difficult to figure out what you are trying to accomplish. > e <- read.table("file1.txt", header=TRUE,row.names=1) > g <- read.table("file2.txt", header=TRUE,row.names=1) > e1<-exp[1,] What's "exp"? Also it's dangerous to use an R function as a variable name. Most of the time R can tell the difference, but in some cases it cannot. > g1<-geno[1,] What's "geno"? > d1<-data.frame(g, e) d1 is now e and g cbind'ed together? > summary(glm(e1 ~ g1, data=d1)) Are "e1" and "g1" elements of "d1"? From what you've told us, I don't know where the error is occurring. Also, if you are having errors, you can more easily isolate the problem by doing: fit <- glm(e1 ~ g1, data = d1) summary(fit) This will at least tell you the problem is in your call to "glm" and not "summary.glm". --sundar P.S. Please (re-)read the POSTING GUIDE. Most of the time you will figure out problems such as these on your own during the process of creating a reproducible example. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html