[BioC] Beginner help

James MacDonald jmacdon at med.umich.edu
Thu Dec 30 23:01:13 CET 2004

Unfortunately there is not one source of all information about R and
Bioconductor (and those that do exist are not always novice-friendly).
My usual method of figuring out how to do something starts with the help
pages. If I know the function, I start with ?function-name to view the
help page. If I don't know if a function actually exists, I will try
help.search(), using some keyword that I think is a reasonable thing to

If I have an error or warning that I don't understand, I will usually
google it, prepending with either an R or BioC depending on if I think
the problem is in base R or a BioC package (there are more elegant ways
to search; Jonathon Baron has a search page on www.r-project.org, and I
believe there is something similar on BioC. However, this method works
reasonably well and is quicker for me.). Usually somebody has already
asked a similar question and received an answer.

If this doesn't work, then I resort to looking at the functions,
possibly using traceback() if there was an error. This is useful for me
because I do a bit of programming in R, so seeing how smart people do
things always helps me to improve. This is really only useful if you
aspire to making your own functions. If you just want to get existing
things to work correctly, the last resort is to ask on either r-help or
the BioC listserv (but not both).



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> Toni-Ann Mistretta <toniannm at bcm.tmc.edu> 12/30/04 12:26 PM >>>
Many thanks Jim! That seems to have done the trick and will be a useful

So next question is -  How do you know that  - painful extraction of 
information over time?  or somewhere you can lead me to?

Thanks again,


At 11:17 AM 12/30/2004, James MacDonald wrote:
>Almost always when you see a message like that, the first course of
>action is the following:
>install.packages2("bioclabs") ## or whatever you are missing
>This should hunt down the package you are looking for and install it
>along with any packages it may depend on. Much better than a manual
>for the package.
>James W. MacDonald
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
> >>> Toni-Ann Mistretta <toniannm at bcm.tmc.edu> 12/30/04 11:10 AM >>>
>At 09:33 AM 12/30/2004, you wrote:
> > >    I have been reading and trying to work through some of the
> > > tutorials available for R and Bioconductor.  I seem to be spending
> > > time working around commands that are no longer recognized in
> > version
> > > of R.   Are there ways around this?  Newer tutorial materials? 
> > > materials would be particular helpful (e.g. End2EndLab)  but many
> > > associated files and commands do not work with newer versions of
> > > there updated files somewhere?
> >
> >Can you give specific examples of what is not working?  It is hard to
> >you advice w/o knowing exactly what you're talking about.
>I start End2End Lab but when I get to  library(bioclabs) I get this
>Error in library(bioclabs) : There is no package called 'bioclabs'
>I tried to find bioclabs but have not had any success.  Seems I am
>more time trying to make something work then actually learning
>Bioconductor.  Of course in this process I am learning a lot about
>Bioconductor, but not what I really need to know.
>What I really need is a R/Bioconductor for dummies book  that has
>I can work through :)
>Toni-Ann Mistretta, Ph.D.
>Baylor College of Medicine
>Houston, Texas 77030
>         [[alternative HTML version deleted]]
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Electronic Mail is not secure, may not be read every day, and should
>be used for urgent or sensitive issues.

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