From: Hu, Ying (NIH/NCI) <yhu_at_mail.nih.gov>

Date: Fri 19 Aug 2005 - 00:38:34 EST

Date: Fri 19 Aug 2005 - 00:38:34 EST

# solution

d1<-data.frame(g[1,], e[1,])

fit<-glm(e[1,] ~ g[1,], data=d1)

summary(fit)

I am not sure that is the best solution.

Thanks again,

Ying

On Wed, 2005-08-17 at 17:22 -0500, Sundar Dorai-Raj wrote:

*>
*

> 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
*

Hi Ying,

That error message is likely caused by having a data.frame on the right hand side (rhs) of the formula. You can't have a data.frame on the rhs of a formula and g1 is still a data frame even if you only choose the first row, e.g.:

dat <- as.data.frame(matrix(100, 10, 10))
class(dat[1, ])

[1] "data.frame"

You could try:

glm(e1 ~ ., data=g1[1, ])

and see if that works, but as Sundar notes, your post is a little difficult to follow, so this may not do what you were trying to achieve.

**HTH
**
Gav

*>
*

> 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

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