Re: [R] do glm with two data sets

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