Bioconductor - Posting Guide (original) (raw)

General advise to posting on the Bioconductor help sites. Please remember when posting a question or response to abide by theBioconductor Code of Conduct.

Revised: 1 Dec, 2023

• Why
• Key points
• Communication with Package Maintainers
• Before Posting
• Composing
• Replying

Why?

• Well-formed questions attract better responses and help save everyone’s time.
• Please remember that the helpers on the support site are volunteers who are often quite knowledgeable about Bioconductor, but won’t know what you have done already, nor what you are trying to do. The key points below are intended to help you give enough information that an experienced person could provide a useful answer without requesting more information.

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Key points

• Use the latest Bioconductor release version. Ensure that your packages are up-to-date.
• Post all of your R code.
• Include a copy of all output including any error or warning messages that appeared in R.
• If your question involves experimental data, include an example of the sample-level covariate data (one row per sample, one column per covariate). If it would help answer your technical question, and can be shared, explain the motivation behind your experiment.
• Always paste the output of sessionInfo() at the end of your post.
• If possible, provide a minimal, self-contained example that someone else can cut-and-paste into a new R session to reproduce your problem.
• If the example produces an error, provide the output oftraceback() after the error occurs.

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Communication with package maintainers

• Tag your post with the names of the appropriate packages. Putting the correct tag is important, as this triggers an automatic email from the system to the package maintainer(s). Capitalization doesn’t matter, but spelling does matter for the package tags.
• Do not email the package maintainer directly. As much as possible, keep all conversations on the support site, and do not revert to email unless indicated by the other party. Some package maintainers have an alternate URL for bug reports, found under BugReports on the package landing page.
• Why? Because the support site is public and searchable, it acts as an archive providing benefit to other users who may face similar errors or issues.

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Before posting

• Read the vignettes for the package in question usingbrowseVignettes("somepkg"). Search the vignette text for sections relevant to your question.
• Read the relevant R documentation. If you are having trouble with function somefunc(), read the relevant sections of ?somefunc, including the sections about function arguments and function output.
• Search the support site for similar posts. The best way to search the support site is using Google by starting with site:support.bioconductor.org followed by a space and a set of keywords and the package name.
• Ensure that your question is on topic. The Bioconductor support site is intended primarily for helping people with questions about using_Bioconductor_ software. Questions about non-_Bioconductor_ R packages or general statistics should be asked on_R_-help orStackoverflow. Questions about bioinformatics in general, but not about Bioconductor packages can be posted to Biostars.

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Composing

• Use an informative post title. This will help attract responders and helps others when they search the support site. For example, a subject line “time course experiment using limma” is better than just “limma”.
• If you are asking for advice on how to use a particular function or package, then explain fully what documentation you have already read and why this hasn’t yet fully answered your question. This allows a responder to answer your specific question instead of simply referring you to the existing documentation.
• As mentioned above, tag your post with the names of the appropriate packages.
• Include code chunks with all output. Use a leading and trailing triple backtick to indicate a code chunk (```). You can directly copy and paste code from your console inbetween the backticks.
• Always include a code chunk with the results of sessionInfo(). This will indicate what os platform version you are running as well as your versions of R and R/Bioconductor package versions.
• Read over your post. Is it polite and easy to understand? Remember that responses on the Bioconductor support site are from volunteers trying to help.
• There is also a helpful tutorial to using/formatting with the markdown editor. This can be found here
• Package development questions are best asked by sending an email to thebioc-devel list.

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Replying

• Use the Add Comment button to ask for further explanation of answers, or to respond to requests for more information.
• Only use the Add Answer button if you are answering the original question.
• If possible, write an answer that can be understood by readers with different scientific backgrounds, skill levels / skill profiles. Use simple English whenever possible to make your answer accessible to the widest audience.
• When answering a question, consider including some explanation of how you arrived at your solution. This way, you help people not only to solve their problem at hand, but also to help themselves in the future.
• Rudeness and personal attacks are not acceptable.
• Brevity is OK. Consider, though, that information that is obvious to you may be very helpful to others.
• Provide URLs to other relevant threads or web sites.

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