do glm with two data sets

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.