GLM Coding Issue

Hi,

Comments inline:

On Tue, Nov 27, 2012 at 1:00 PM, Craig P O'Connell
<coconnell2 at umassd.edu> wrote:

Dear all,

  I am having a recurring problem when I attempt to conduct a GLM.   
Here is what I am attempting (with fake data):
First, I created a txt file, changed the directory in R (to the  
proper folder containing the file) and loaded the file:

#avoid<-read.table("avoid.txt",header=TRUE);avoid
#  treatment feeding avoid noavoid
#1   control  nofeed     1     357
#2   control    feed     2     292
#3   control     sat     4     186
#4      proc  nofeed    15     291
#5      proc    feed    25     288
#6      proc     sat    17     140
#7       mag  nofeed    87     224
#8       mag    feed    34     229
#9       mag     sat    46     151

I then try to "attach(avoid)" the data, but continue to get an  
error message ( The following object(s) are masked  
_by_ .GlobalEnv :), so to fix this, I do the following:

#newavoid<-avoid
#newavoid                (does this do anything?)

It essentially makes a copy of `avoid` to `newavoid` -- what did you
want it to do?

That having been said, a good rule of thumb is to never use `attach`,
so let's avoid it for now.

Lastly, I have several GLM's I wanted to conduct.  Please see the  
following:

#model1<-glm(cbind(avoid, noavoid)~treatment,data=,family=binomial)

#model2=glm(cbind(avoid, noavoid)~feeding, familiy=binomial)

#model3=glm(cbind(avoid, noavoid)~treatment+feeding,  
familiy=binomial)

`cbind`-ing doesn't make much sense here. What is your target (y)
variable here? are you trying to predict `avoid` or `noavoid` status?

Let's assume you were "predicting" `noavoid` from just `treatment` and
`feeding` (I guess you have more data (rows) than you show), you would
build a model like so:

R> model <- glm(noavoid ~ treatment + feeding, binomial, avoid)

Or to be explicit about the parameters:

R> model <- glm(noavoid ~ treatment + feeding, family=binomial,  
data=avoid)

It would be greatly appreciated if somebody can help me with my  
coding, as you can see I am a novice but doing my best to learn.  I  
figured if I can get model1 to run, I should be able to figure out  
the rest of my models.

Since you're just getting started, maybe it would be helpful for
people writing documentation/tutorials/whatever what needs to be
explained better.

For instance, I'm curious why you thought to `cbind` in your first glm
call, which was:

model1<-glm(cbind(avoid, noavoid)~treatment,data=,family=binomial)

What did you think `cbind`-ing was accomplishing for you? Is there an
example somewhere that's doing that as the first parameter to a `glm`
call?

Also, why just have `data=<nothing>`?

I'm not criticizing, just trying to better understand.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact