Almost always when you see a message like that, the first course of action is the following: library(reposTools) 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 hunt for the package. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Toni-Ann Mistretta <toniannm@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 demos and > > tutorials available for R and Bioconductor. I seem to be spending more > > time working around commands that are no longer recognized in newer > version > > of R. Are there ways around this? Newer tutorial materials? The Lab > > materials would be particular helpful (e.g. End2EndLab) but many of the > > associated files and commands do not work with newer versions of R. Are > > there updated files somewhere? > >Can you give specific examples of what is not working? It is hard to give >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 message Error in library(bioclabs) : There is no package called 'bioclabs' I tried to find bioclabs but have not had any success. Seems I am spending 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 exercises I can work through :) Thanks Toni-Ann Toni-Ann Mistretta, Ph.D. HCOA/BRC Baylor College of Medicine Houston, Texas 77030 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Many thanks Jim! That seems to have done the trick and will be a useful tool. So next question is - How do you know that - painful extraction of information over time? or somewhere you can lead me to? Thanks again, Toni-Ann 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: > >library(reposTools) >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 hunt >for the package. > >HTH, > >Jim > > > >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > >>> Toni-Ann Mistretta <toniannm@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 demos >and > > > tutorials available for R and Bioconductor. I seem to be spending >more > > > time working around commands that are no longer recognized in newer > > version > > > of R. Are there ways around this? Newer tutorial materials? The >Lab > > > materials would be particular helpful (e.g. End2EndLab) but many of >the > > > associated files and commands do not work with newer versions of R. >Are > > > there updated files somewhere? > > > >Can you give specific examples of what is not working? It is hard to >give > >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 >message > >Error in library(bioclabs) : There is no package called 'bioclabs' > >I tried to find bioclabs but have not had any success. Seems I am >spending >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 >exercises >I can work through :) > >Thanks > >Toni-Ann > >Toni-Ann Mistretta, Ph.D. >HCOA/BRC >Baylor College of Medicine >Houston, Texas 77030 > > > > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should not >be used for urgent or sensitive issues. [[alternative HTML version deleted]]

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 use. 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). HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Toni-Ann Mistretta <toniannm@bcm.tmc.edu> 12/30/04 12:26 PM >>> Many thanks Jim! That seems to have done the trick and will be a useful tool. So next question is - How do you know that - painful extraction of information over time? or somewhere you can lead me to? Thanks again, Toni-Ann 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: > >library(reposTools) >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 hunt >for the package. > >HTH, > >Jim > > > >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > >>> Toni-Ann Mistretta <toniannm@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 demos >and > > > tutorials available for R and Bioconductor. I seem to be spending >more > > > time working around commands that are no longer recognized in newer > > version > > > of R. Are there ways around this? Newer tutorial materials? The >Lab > > > materials would be particular helpful (e.g. End2EndLab) but many of >the > > > associated files and commands do not work with newer versions of R. >Are > > > there updated files somewhere? > > > >Can you give specific examples of what is not working? It is hard to >give > >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 >message > >Error in library(bioclabs) : There is no package called 'bioclabs' > >I tried to find bioclabs but have not had any success. Seems I am >spending >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 >exercises >I can work through :) > >Thanks > >Toni-Ann > >Toni-Ann Mistretta, Ph.D. >HCOA/BRC >Baylor College of Medicine >Houston, Texas 77030 > > > > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should not >be used for urgent or sensitive issues. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.