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Bioconductor Posting Guide

Before sending mail to the list

  1. Read the relevant R documentation. If you are having trouble with function somefunc, try help("somefunc"). If you are searching for a function, try help.search("somefunc"). Alternatively, use help.start() to start the HTML search engine.

  2. Make sure your question hasn't already been answered by searching the FAQ.

  3. Read the vignette(s) for the package(s) you are using:

  4. ## List available vignettes for "somepkg"
    vignette(package="somepkg")
    ## open the "intro" vingnet in "somepkg"
    vignette("intro", package="somepkg")
  5. Check the BioConductor mailing list archives and the R-help mailing list archive to see if your question has been asked (and answered) already.

  6. Try a Google search.

  7. See if the error is reproducible when you run the code again from a fresh R session or if you use a slightly different dataset.

While sending mail to the list

  1. Start a new mail instead of replying to an existing mail and changing the subject.

  2. Use an informative subject line. This will help attract responders and also helps others in the future when they search the archives.

  3. Identify yourself. Anonymous postings are much less likely to get responses.
  4. Give a simple and reproducible example if possible. If there is an error message, please include it along with operating system, R version and relevant package versions. Use sessionInfo() to show versions of R and all attached packages.

  5. Choose your audience appropriately:
    BioConductor mailing list
    For general question using Bioconductor packages and bioinformatics. Note that questions that are conceptual in nature are welcomed here.
    Direct email to package maintainer
    Alternatively, if the package is in development version, you can try asking the package authors directly.
    R-help mailing list
    R-help is more suited questions that have to do with the underlying R program.
    BioC-devel and R-devel
    These lists are for discussing code development and other more technical stuff.
  6. Read your mail again. Have you stated your goal and objectives clearly? Keep your mail as precise and concise as you can.

Some optional settings

  1. Please use plain text instead of HTML as will be easier to detect spam and malicious softwares. Plain texts are also smaller in size and easier to read.
  2. Ensure that your lines are wrapped at about 72 characters, which makes postings more readable. Otherwise one paragraph will be rendered on one long line when someone replies to your mail. See this webpage (http://expita.com/nomime.html) for instructions on how to configure your mail client to send plain text and line wrapping.
  3. Try to ensure that your codes are readable. Long lines of codes should be simplified and have new lines at the appropriate places. Note that as a consequence of line wrapping, your codes may wrap at unexpected places.
  4. The only allowed attachment is PS, PDF, JPG, PNG (?) and mail must be less that 40 kb in size. Otherwise your mail will require administrator approval before being posted.
  5. Learn to write in clear, grammatical, correctly-spelled language. If your mail client supports a spell check, please utilise it. Otherwise compose in a word composer beforehand that has these features.
  6. Read over your mail. Is it easy to understand and does your mail sound polite? Remember that BioConductor and its mailing list is created and maintained by volunteers who are not paid technical support people.

When replying to mail on the list

  1. Respond to everyone in the list, which ensures that your response is archived.
  2. If possible, write an answer that can be understood by readers with different scientific backgrounds and skill levels / skill profiles.
  3. When answering a question, consider including some explanation of how you arrived at your solution (rather than just writing a solution). This way, you help people not only to solve their problem at hand, but also to help themselves in the future.
  4. Rudeness and ad hominem comments are not acceptable.
  5. Brevity is OK. Consider, though, that information that is obvious and not worth mentioning to you may be very helpful to others.
  6. If you believe the issue has been discussed before, please give the URL of the relevant thread or website.

Why a posting guide ?

  1. Good questions attract good responses.
  2. The act of formulating good questions can help to solve the problem itself.
  3. Good questions avoid wasting other people's time and avoids embarrassment.

Acknowledgements

This posting guide has been heavily adapted from the R-help mailing list posting guide (http://www.r-project.org/posting-guide.html), various comments and suggestions by BioConductor posters and inspired by Eric Raymonds' essay on How To Ask Questions The Smart Way.

News
2008-05-01

BioC 2.2, consisting of 260 packages and designed to work with R 2.7.0, was released today.

2008-03-04

BioConductor release scheduled for 30 April 2008.