[R] do glm with two data sets

[Sundar Dorai-Raj]

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.