gmane.science.biology.informatics.conductor

Mark Kimpel | 16 May 02:32

question on affyQCReport vignette

I am a satistified user of affyQCReport and want to make sure that I include
the appropriate citations in a paper I am submitting. As this package is
sort of a wrapper for some other packages and the vignette does not include
any references beyond that of Gautier, et al, which describes the affy
package, could someone be kind enough to supply me with the appropriate
citations?

In general, it is sort of a pet peeve of mine that developers rightly want
their work cited, but too often I feel that the citation information on the
help(package == "foo") page is imcomplete. Would it be presumtuous to ask
for developers to include a handy list of citations for their packages,
package dependencies, etc. as part of the general help page for their
package? I don't know what the official R/BioC policy is on this, but it
would be extremely helpful both to users and those whose original ideas are
incorporated into R/BioC.

And, if I"ve missed something obvious, point me in the right direction,
spank me with a wet noodle and accept my apologies.

Thanks,
Mark

--

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

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Keith Satterley | 16 May 06:23

Re: question on affyQCReport vignette

Hi Mark,

are you aware of the citation("package_name") command. See limma package for an 
example. I notice that the affyQCReport citation is auto generated.

Perhaps more package authors should be encouraged to take control of what 
citation() reports.

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
=======================

Mark Kimpel wrote:
> I am a satistified user of affyQCReport and want to make sure that I include
> the appropriate citations in a paper I am submitting. As this package is
> sort of a wrapper for some other packages and the vignette does not include
> any references beyond that of Gautier, et al, which describes the affy
> package, could someone be kind enough to supply me with the appropriate
> citations?
> 
> In general, it is sort of a pet peeve of mine that developers rightly want
> their work cited, but too often I feel that the citation information on the

(Continue reading)

headers

Mark Kimpel | 16 May 19:54

Re: question on affyQCReport vignette

Thanks for reminding me about the citation function, but what I had in mind
was more than just a way to cite the package itself. The package authors
rely on published findings of others, as well as other packages that they
depend on, and it would be nice to make sure credit is given where credit is
due. Although each user could (and in the absence of other information
should) track down all the papers that contribute to a package, I think it
would be nice if the package maintainers include that information in the
output to citation("foo"). The developers/maintainers are in the best
position to know what papers they have relied on and, lets face it, there is
less work for everyone if the maintainer does it once and says all his/her
users the work of doing it hundreds of times for themselves.

Mark

On Fri, May 16, 2008 at 12:23 AM, Keith Satterley <keith@...> wrote:

> Hi Mark,
>
> are you aware of the citation("package_name") command. See limma package
> for an example. I notice that the affyQCReport citation is auto generated.
>
> Perhaps more package authors should be encouraged to take control of what
> citation() reports.
>
> cheers,
>
> Keith
>
> ========================
> Keith Satterley

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