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

Date: Fri 19 Aug 2005 - 00:47:44 EST

*>
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*>
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> Hi Ying,

*>
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*> That error message is likely caused by having a data.frame on the right
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*> hand side (rhs) of the formula. You can't have a data.frame on the rhs
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*> of a formula and g1 is still a data frame even if you only choose the
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*> first row, e.g.:
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*>
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*> dat <- as.data.frame(matrix(100, 10, 10))
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*> class(dat[1, ])
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*> [1] "data.frame"
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*>
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*> You could try:
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*>
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*> glm(e1 ~ ., data=g1[1, ])
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*>
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*> and see if that works, but as Sundar notes, your post is a little
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*> difficult to follow, so this may not do what you were trying to achieve.
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*>
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*> HTH
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*>
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*> Gav
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*>
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*>
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*>
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> http://www.R-project.org/posting-guide.html

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 Fri Aug 19 01:08:46 2005

Date: Fri 19 Aug 2005 - 00:47:44 EST

Hu, Ying (NIH/NCI) wrote:

> Thanks for your help.

*>
**> # read the two data sets
**> e <- as.matrix(read.table("file1.txt", header=TRUE,row.names=1))
**> g <- as.matrix(read.table("file2.txt", header=TRUE,row.names=1))
**>
**> # 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
**>
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Hi, Ying,

What's wrong with this solution? Do you still get an error? What is your primary goal?

A couple of points:

- It's better to use names in your data.frame:

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

Then in glm:

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

2. Also, you may just be giving us a toy example, but if you don't specify a family argument in glm then you are simply getting the least squares. In that case you should use ?lm instead.

**HTH,
**
--sundar

*>
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> -----Original Message-----

*> From: Gavin Simpson [mailto:gavin.simpson@ucl.ac.uk]
**> Sent: Wednesday, August 17, 2005 7:01 PM
**> To: Sundar Dorai-Raj
**> Cc: Hu, Ying (NIH/NCI); r-help@stat.math.ethz.ch
**> Subject: Re: [R] do glm with two data sets
**>
**> 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,

>>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

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 Fri Aug 19 01:08:46 2005

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