[BioC] topGO desperation

[James W. MacDonald]

Hi Christian,

On 5/13/2013 5:22 AM, Oertlin, Christian (Stud. FHML) wrote:
> Dear mr/mrs,
>
> First of all,  I am a new R user. ;)
> I am currently working with GOdata, and I want to try to map this data visually with R using topGO.
>
> My problem begins in the very beginning. I cannot find to load my data into R that it get's recognised as library  or anything else I can work with. So my question what do I have to do to load my data (GO file) into topGO.
>
> Here is my script so far, not much but a beginning.
>
> #set working directory
> setwd("/Users/christianoertlin/Desktop/Stage files/R")
>
> #Use soure bioconductor.org<http://bioconductor.org>
> source("http://bioconductor.org/biocLite.R")
>   #open library
> library(topGO)
> library (AnnotationDbi)
>   #load GO file into R here are my troubles

As a first step, you should read 'An Introduction to R' 
(http://cran.r-project.org/doc/manuals/r-release/R-intro.pdf). You will 
not be able to get very far with BioC if you don't know how to load data 
into R. Being at least semi-competent with R itself is a crucial aspect 
to using BioC, so learning the basics is time well spent.

Additionally, although you have given some code here, you aren't giving 
us much to go on. What is your GO file? What is in it? What have you 
tried to read it into R? Did it fail? If so, what was the error message?

Best,

Jim

>
>
> Kind regards,
> Christian Oertlin
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099