Question: no BioConductor posting guide
0
gravatar for Adaikalavan Ramasamy
14.2 years ago by
Adaikalavan Ramasamy1.8k wrote:
The instruction to read the posting guide is appended to every message that appears in R-help mailing list as follows : ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html But no link to the posting guide in the footed of messages that appear to BioConductor mail. Instead we get : _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Is this because no posting guide suitable for BioConductor has been developed ? I am sure one can easily adapt from the R-help one. Thank you. Regards, Adai
• 553 views
ADD COMMENTlink modified 14.2 years ago by Liaw, Andy360 • written 14.2 years ago by Adaikalavan Ramasamy1.8k
Answer: no BioConductor posting guide
0
gravatar for A.J. Rossini
14.2 years ago by
A.J. Rossini210
A.J. Rossini210 wrote:
On Apr 8, 2005 1:09 PM, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > > Is this because no posting guide suitable for BioConductor has been > developed ? I am sure one can easily adapt from the R-help one. Why don't you take the first stab at it? best, -tony "Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes" (AJR, 4Jan05). A.J. Rossini blindglobe@gmail.com
ADD COMMENTlink written 14.2 years ago by A.J. Rossini210
Dear Tony, Do you have any comments on the draft of the BioConductor posting guide ( http://tinyurl.com/3kswc ). Thank you. Regards, Adai On Fri, 2005-04-08 at 13:53 +0200, A.J. Rossini wrote: > On Apr 8, 2005 1:09 PM, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > > > > Is this because no posting guide suitable for BioConductor has been > > developed ? I am sure one can easily adapt from the R-help one. > > Why don't you take the first stab at it? > > best, > -tony > > "Commit early,commit often, and commit in a repository from which we can easily > roll-back your mistakes" (AJR, 4Jan05). > > A.J. Rossini > blindglobe@gmail.com >
ADD REPLYlink written 14.2 years ago by Adaikalavan Ramasamy1.8k
At first glance it seems fine to me. I would include * Link to the R-FAQ and the R-FAQ for MacOS * Checking capabilities() * Explicitly tell whether one is using the release version or the devel version. Kasper On Wed, Apr 13, 2005 at 01:07:39PM +0100, Adaikalavan Ramasamy wrote: > Dear Tony, > > Do you have any comments on the draft of the BioConductor posting guide > ( http://tinyurl.com/3kswc ). > > Thank you. > > Regards, Adai > > > On Fri, 2005-04-08 at 13:53 +0200, A.J. Rossini wrote: > > On Apr 8, 2005 1:09 PM, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > > > > > > Is this because no posting guide suitable for BioConductor has been > > > developed ? I am sure one can easily adapt from the R-help one. > > > > Why don't you take the first stab at it? > > > > best, > > -tony > > > > "Commit early,commit often, and commit in a repository from which we can easily > > roll-back your mistakes" (AJR, 4Jan05). > > > > A.J. Rossini > > blindglobe@gmail.com > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
ADD REPLYlink written 14.2 years ago by Kasper Daniel Hansen630
Looks fine to me, modulo Kasper's suggestions, which are good. Probably someone else with more brainpower or focus right now should comment as well, I'm preoccupied with a bit too much. On 4/13/05, Kasper Daniel Hansen <k.hansen@biostat.ku.dk> wrote: > At first glance it seems fine to me. I would include > * Link to the R-FAQ and the R-FAQ for MacOS > * Checking capabilities() > * Explicitly tell whether one is using the release version or the devel > version. > > Kasper > > On Wed, Apr 13, 2005 at 01:07:39PM +0100, Adaikalavan Ramasamy wrote: > > Dear Tony, > > > > Do you have any comments on the draft of the BioConductor posting guide > > ( http://tinyurl.com/3kswc ). > > > > Thank you. > > > > Regards, Adai > > > > > > On Fri, 2005-04-08 at 13:53 +0200, A.J. Rossini wrote: > > > On Apr 8, 2005 1:09 PM, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > > > > > > > > Is this because no posting guide suitable for BioConductor has been > > > > developed ? I am sure one can easily adapt from the R-help one. > > > > > > Why don't you take the first stab at it? > > > > > > best, > > > -tony > > > > > > "Commit early,commit often, and commit in a repository from which we can easily > > > roll-back your mistakes" (AJR, 4Jan05). > > > > > > A.J. Rossini > > > blindglobe@gmail.com > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > Kasper Daniel Hansen, Research Assistant > Department of Biostatistics, University of Copenhagen > > -- best, -tony "Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes" (AJR, 4Jan05). A.J. Rossini blindglobe@gmail.com
ADD REPLYlink written 14.2 years ago by A.J. Rossini210
Answer: no BioConductor posting guide
0
gravatar for Seth Falcon
14.2 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"A.J. Rossini" <blindglobe@gmail.com> writes: > On Apr 8, 2005 1:09 PM, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > >> >> Is this because no posting guide suitable for BioConductor has been >> developed ? I am sure one can easily adapt from the R-help one. > > Why don't you take the first stab at it? I'm +1 on this idea :-) If someone creates a Bioconductor specific posting guide (and there is reasonable consensus in the community that it is liked) I will get it posted and "footed"? + seth
ADD COMMENTlink written 14.2 years ago by Seth Falcon7.4k
Talk about things backfiring ... (sigh) OK, I will modify/create one for BioC. I intend on making it on a wikipage so that everyone who wants to, can contribute to it. I will hopefully post the URL in a few days. I also plan on diverting this to the BioC-devel as I feel it will be more appropriate there. Anyone who wants to follow this, see you there. Regards, Adai On Fri, 2005-04-08 at 07:04 -0700, Seth Falcon wrote: > "A.J. Rossini" <blindglobe@gmail.com> writes: > > > On Apr 8, 2005 1:09 PM, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > > > >> > >> Is this because no posting guide suitable for BioConductor has been > >> developed ? I am sure one can easily adapt from the R-help one. > > > > Why don't you take the first stab at it? > > I'm +1 on this idea :-) > > If someone creates a Bioconductor specific posting guide (and there is > reasonable consensus in the community that it is liked) I will get it > posted and "footed"? > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLYlink written 14.2 years ago by Adaikalavan Ramasamy1.8k
Answer: no BioConductor posting guide
0
gravatar for Adaikalavan Ramasamy
14.2 years ago by
Adaikalavan Ramasamy1.8k wrote:
See comments below. On Fri, 2005-04-08 at 14:15 +0100, Jan T. Kim wrote: > Hi Adai, <snip> > But is there such a problem in BioC? Personally, I'm quite a happy > BioC subscriber and don't see any need to try and control the amount > of thoughtless postings here. As you mention below, this is an inter-disciplinary field and thus sometimes I find excellent questions posted here do not attract sufficient responses because they are poorly written. But maybe this is a case of "R has one, so why not BioConductor" envy ? > It is very important to consider the fact that BioC is an > interdisciplinary audience much more than r-help. If bioscientists > (with a spotty statistics background) perceive BioC as a bunch of > arrogant know-it-alls, this is detrimental to interdisciplinary > communication at the core of BioC's subject area. This is an important point. > Therefore, if a BioC posting guide is written, I strongly recommend to > take great care to avoid any suspicion of arrogance and unwillingness > to entertain the sometimes difficult / boring / seemingly unknowledgeable > processes of interdisciplinary communication. As a biologist who has > moved into computational biology, I've seen a few times how easy it is > to be perceived as arrogant, and how difficult it is to convince people > otherwise once they got this impression. Again an excellent point. I have taken this into consideration and have hopefully incorporated into the posting guide. I look forward towards your comments and ideas. > It seems to me that the best way to avoid this risk is to not have a > posting guide, at least not one in the r-help style -- unless there are Yes, I have taken some of the more important points from R-help posting and rearranged it to be more "friendly". > strong reasons in favour of that. But if it ain't broke, don't fix it. True. But it seems that a few people have expressed a desire for a posting guide. So if not me, then someone else will fix it. > Best regards, Jan
ADD COMMENTlink written 14.2 years ago by Adaikalavan Ramasamy1.8k
Answer: no BioConductor posting guide
0
gravatar for Matthew  Hannah
14.2 years ago by
Matthew Hannah940 wrote:
Good idea, couple of minor suggestions. I'd change 1 or 3 this to something along these lines to stress that all packages can be browsed for functions, their definitions and other package documentation using the html help. This is useful even if you don't know exactly what a function is or to get an overview of what a package can do. Alternatively use help.start() to start the HTML help where you can search functions or browse packages for documentation, function listings and definitions. and/or Read any relevant BioConductor documentations such as the vignettes (http://www.bioconductor.org/viglistingindex.html). Other materials can be found on the "Documents" section of the main BioConductor webpage or by browsing the package listings in the HTML help. Maybe point 4 to include the link for the bioC archives as it's sometimes easier to use this to follow threads or to find something. Checked the BioConductor mailing archives (http://files.protsuggest.org/cgi-bin/biocond.cgi) or the R-help mailing archives (http://maths.newcastle.edu.au/~rking/R/) if your question has been asked (and answered) before. The BioConductor mailing archives can also be browsed by date, author or thread (https://www.stat.math.ethz.ch/pipermail/bioconductor/). Maybe also mention that the functions traceback() and debug() are useful for identifying the source of the problem. This would also help save the inevitable 'what does traceback() say' reply. In the optional stuff I would say that the attachments can be viewed on the html archives as sometimes when attachments are included I wonder how many BioC users are actually aware they can be viewed. 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. 4. The only allowed attachments are PS, PDF, JPG, PNG (?) and mail must be less that 40 kb in size. Otherwise your mail will require administrator approval before being posted. Be aware that attachments are not included in the Bioconductor Digest emails but can be viewed on the mailing archives (https://www.stat.math.ethz.ch/pipermail/bioconductor/). Finally, to help Gordon out how about 'if your question regards Limma designs, contrasts or statistics then have you checked the latest limma users guide' ;-) HTH, Matt #### >Dear Tony, > >Do you have any comments on the draft of the BioConductor posting guide >( http://tinyurl.com/3kswc ). > >Thank you. > >Regards, Adai
ADD COMMENTlink written 14.2 years ago by Matthew Hannah940
I agree with most of these points. But in fact I feel that it belongs to a proper "how to get help with Bioconductor" guide, which I have had some plans for writing for a while (I do not have time to do it within say the next month or so). Basically there are so many techniques that it really requires a small guide. But perhaps the points below should be included in the posting guide. We can always revise it, if and when the help-guide gets made by me or another helpful soul. Kasper On Thu, Apr 14, 2005 at 09:45:17AM +0200, Matthew Hannah wrote: > Good idea, couple of minor suggestions. > > I'd change 1 or 3 this to something along these lines to stress that all > packages can be browsed for functions, their definitions and other > package documentation using the html help. This is useful even if you > don't know exactly what a function is or to get an overview of what a > package can do. > > Alternatively use help.start() to start the HTML help where you can > search functions or browse packages for documentation, function listings > and definitions. > > and/or > > Read any relevant BioConductor documentations such as the vignettes > (http://www.bioconductor.org/viglistingindex.html). Other materials can > be found on the "Documents" section of the main BioConductor webpage or > by browsing the package listings in the HTML help. > > > Maybe point 4 to include the link for the bioC archives as it's > sometimes easier to use this to follow threads or to find something. > Checked the BioConductor mailing archives > (http://files.protsuggest.org/cgi-bin/biocond.cgi) or the R-help mailing > archives (http://maths.newcastle.edu.au/~rking/R/) if your question has > been asked (and answered) before. The BioConductor mailing archives can > also be browsed by date, author or thread > (https://www.stat.math.ethz.ch/pipermail/bioconductor/). > > > Maybe also mention that the functions traceback() and debug() are useful > for identifying the source of the problem. This would also help save the > inevitable 'what does traceback() say' reply. > > > > In the optional stuff I would say that the attachments can be viewed on > the html archives as sometimes when attachments are included I wonder > how many BioC users are actually aware they can be viewed. > 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. > > 4. The only allowed attachments are PS, PDF, JPG, PNG (?) and mail must > be less that 40 kb in size. Otherwise your mail will require > administrator approval before being posted. Be aware that attachments > are not included in the Bioconductor Digest emails but can be viewed on > the mailing archives > (https://www.stat.math.ethz.ch/pipermail/bioconductor/). > > > Finally, to help Gordon out how about 'if your question regards Limma > designs, contrasts or statistics then have you checked the latest limma > users guide' ;-) > > HTH, > Matt > > > #### > >Dear Tony, > > > >Do you have any comments on the draft of the BioConductor posting guide > >( http://tinyurl.com/3kswc ). > > > >Thank you. > > > >Regards, Adai > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
ADD REPLYlink written 14.2 years ago by Kasper Daniel Hansen630
Dear Matthew Hannah and Kasper Hansen, Thank you for your comments. I agree with Kasper that the "Howto get help in BioConductor" should be kept a separate section. I intend the posting guide to concise in order to encourage people to read it. In view of the recent comments, I think it might be be useful to have two separate sections on "HOWTO get help with R and BioConductor" and "HOWTO report a problem efficiently" and link to the posting guide and different groups of people would view it differently. It would be another couple of weeks before I am able to do this. If anyone would like to please feel free to add on to the wiki. Thank you. Regards, Adai On Thu, 2005-04-14 at 10:56 +0200, Kasper Daniel Hansen wrote: > I agree with most of these points. But in fact I feel that it belongs to > a proper "how to get help with Bioconductor" guide, which I have had > some plans for writing for a while (I do not have time to do it within > say the next month or so). Basically there are so many techniques that > it really requires a small guide. > > But perhaps the points below should be included in the posting guide. We > can always revise it, if and when the help-guide gets made by me or > another helpful soul. > > Kasper > > > > On Thu, Apr 14, 2005 at 09:45:17AM +0200, Matthew Hannah wrote: > > Good idea, couple of minor suggestions. > > > > I'd change 1 or 3 this to something along these lines to stress that all > > packages can be browsed for functions, their definitions and other > > package documentation using the html help. This is useful even if you > > don't know exactly what a function is or to get an overview of what a > > package can do. > > > > Alternatively use help.start() to start the HTML help where you can > > search functions or browse packages for documentation, function listings > > and definitions. > > > > and/or > > > > Read any relevant BioConductor documentations such as the vignettes > > (http://www.bioconductor.org/viglistingindex.html). Other materials can > > be found on the "Documents" section of the main BioConductor webpage or > > by browsing the package listings in the HTML help. > > > > > > Maybe point 4 to include the link for the bioC archives as it's > > sometimes easier to use this to follow threads or to find something. > > Checked the BioConductor mailing archives > > (http://files.protsuggest.org/cgi-bin/biocond.cgi) or the R-help mailing > > archives (http://maths.newcastle.edu.au/~rking/R/) if your question has > > been asked (and answered) before. The BioConductor mailing archives can > > also be browsed by date, author or thread > > (https://www.stat.math.ethz.ch/pipermail/bioconductor/). > > > > > > Maybe also mention that the functions traceback() and debug() are useful > > for identifying the source of the problem. This would also help save the > > inevitable 'what does traceback() say' reply. > > > > > > > > In the optional stuff I would say that the attachments can be viewed on > > the html archives as sometimes when attachments are included I wonder > > how many BioC users are actually aware they can be viewed. > > 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. > > > > 4. The only allowed attachments are PS, PDF, JPG, PNG (?) and mail must > > be less that 40 kb in size. Otherwise your mail will require > > administrator approval before being posted. Be aware that attachments > > are not included in the Bioconductor Digest emails but can be viewed on > > the mailing archives > > (https://www.stat.math.ethz.ch/pipermail/bioconductor/). > > > > > > Finally, to help Gordon out how about 'if your question regards Limma > > designs, contrasts or statistics then have you checked the latest limma > > users guide' ;-) > > > > HTH, > > Matt > > > > > > #### > > >Dear Tony, > > > > > >Do you have any comments on the draft of the BioConductor posting guide > > >( http://tinyurl.com/3kswc ). > > > > > >Thank you. > > > > > >Regards, Adai > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLYlink written 14.2 years ago by Adaikalavan Ramasamy1.8k
Answer: no BioConductor posting guide
0
gravatar for Liaw, Andy
14.2 years ago by
Liaw, Andy360
Liaw, Andy360 wrote:
Hi Adai, Just one editorial comment: It seems to me the guide is heavy on `how', but says very little about `why'. I think for newcomers it may be helpful to know why they are being asked to follow the guide (I guess mostly to save bandwidth and people's time). Just my $0.02 (which went up in value yesterday!) Andy > From: Adaikalavan Ramasamy > > Dear Matthew Hannah and Kasper Hansen, > > Thank you for your comments. I agree with Kasper that the "Howto get > help in BioConductor" should be kept a separate section. I intend the > posting guide to concise in order to encourage people to read it. > > In view of the recent comments, I think it might be be useful to have > two separate sections on "HOWTO get help with R and BioConductor" and > "HOWTO report a problem efficiently" and link to the posting guide and > different groups of people would view it differently. It would be > another couple of weeks before I am able to do this. If anyone would > like to please feel free to add on to the wiki. > > Thank you. > > Regards, Adai > > > On Thu, 2005-04-14 at 10:56 +0200, Kasper Daniel Hansen wrote: > > I agree with most of these points. But in fact I feel that > it belongs to > > a proper "how to get help with Bioconductor" guide, which I > have had > > some plans for writing for a while (I do not have time to > do it within > > say the next month or so). Basically there are so many > techniques that > > it really requires a small guide. > > > > But perhaps the points below should be included in the > posting guide. We > > can always revise it, if and when the help-guide gets made by me or > > another helpful soul. > > > > Kasper > > > > > > > > On Thu, Apr 14, 2005 at 09:45:17AM +0200, Matthew Hannah wrote: > > > Good idea, couple of minor suggestions. > > > > > > I'd change 1 or 3 this to something along these lines to > stress that all > > > packages can be browsed for functions, their definitions and other > > > package documentation using the html help. This is useful > even if you > > > don't know exactly what a function is or to get an > overview of what a > > > package can do. > > > > > > Alternatively use help.start() to start the HTML help > where you can > > > search functions or browse packages for documentation, > function listings > > > and definitions. > > > > > > and/or > > > > > > Read any relevant BioConductor documentations such as the > vignettes > > > (http://www.bioconductor.org/viglistingindex.html). Other > materials can > > > be found on the "Documents" section of the main > BioConductor webpage or > > > by browsing the package listings in the HTML help. > > > > > > > > > Maybe point 4 to include the link for the bioC archives as it's > > > sometimes easier to use this to follow threads or to find > something. > > > Checked the BioConductor mailing archives > > > (http://files.protsuggest.org/cgi-bin/biocond.cgi) or the > R-help mailing > > > archives (http://maths.newcastle.edu.au/~rking/R/) if > your question has > > > been asked (and answered) before. The BioConductor > mailing archives can > > > also be browsed by date, author or thread > > > (https://www.stat.math.ethz.ch/pipermail/bioconductor/). > > > > > > > > > Maybe also mention that the functions traceback() and > debug() are useful > > > for identifying the source of the problem. This would > also help save the > > > inevitable 'what does traceback() say' reply. > > > > > > > > > > > > In the optional stuff I would say that the attachments > can be viewed on > > > the html archives as sometimes when attachments are > included I wonder > > > how many BioC users are actually aware they can be viewed. > > > 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. > > > > > > 4. The only allowed attachments are PS, PDF, JPG, PNG (?) > and mail must > > > be less that 40 kb in size. Otherwise your mail will require > > > administrator approval before being posted. Be aware that > attachments > > > are not included in the Bioconductor Digest emails but > can be viewed on > > > the mailing archives > > > (https://www.stat.math.ethz.ch/pipermail/bioconductor/). > > > > > > > > > Finally, to help Gordon out how about 'if your question > regards Limma > > > designs, contrasts or statistics then have you checked > the latest limma > > > users guide' ;-) > > > > > > HTH, > > > Matt > > > > > > > > > #### > > > >Dear Tony, > > > > > > > >Do you have any comments on the draft of the > BioConductor posting guide > > > >( http://tinyurl.com/3kswc ). > > > > > > > >Thank you. > > > > > > > >Regards, Adai > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
ADD COMMENTlink written 14.2 years ago by Liaw, Andy360
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 316 users visited in the last hour