From: Sundar Dorai-Raj <sundar.dorai-raj_at_pdf.com>

Date: Thu 18 Aug 2005 - 08:22:34 EST

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 Received on Thu Aug 18 08:29:24 2005

Date: Thu 18 Aug 2005 - 08:22:34 EST

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 Received on Thu Aug 18 08:29:24 2005

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