[Rd] data set mube S4 class to be submitted to Bioconductor
Dear R Developers, I am developing a package to submit to bioconductor. Right now, a gene-set sample data is saved as a data frame. Each row contains a probe set and its corresponding gene-set name ( mutiple probe -set may map to a gene-set name) . Is this type of data format OK to be submitted to bioconductor? Or I have to make it GeneCollectionSet class? ( If so, I have to change a lot of my R functions). Your resonse is highly appreciated! Lani [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] data set mube S4 class to be submitted to Bioconductor
On 10/12/2010 07:38 AM, lan gao wrote: > Dear R Developers, > > I am developing a package to submit to bioconductor. Right now, a gene-set > sample data is saved as a data frame. Each row contains a probe set and its > corresponding gene-set name ( mutiple probe -set may map to a gene-set name) > . > > Is this type of data format OK to be submitted to bioconductor? Or I have to > make it GeneCollectionSet class? ( If so, I have to change a lot of my R > functions). > > Your resonse is highly appreciated! See the answer to your original post here https://stat.ethz.ch/pipermail/bioconductor/2010-October/035781.html The 'Bioc-devel' list mentioned there is https://stat.ethz.ch/mailman/listinfo/bioc-devel referenced from http://bioconductor.org/help/mailing-list/ Asking on the bioc-devel mailing list will not change the original answer, but is the appropriate place to ask future questions about developing Bioconductor packages. Martin > > > Lani > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] FW: [R] same random numbers in different sessions
From R-help ... >I notice that you have the IPSUR package loaded; you know, just a >shot in the dark here, but did you try not loading it? > >I ask because the vignette is built by making a special choice for >set.seed, and the workspace that ships with the package might be >interacting in an unexpected way. Is it possible that a package can save a set seed and have the effect that users get when they save a workspace with the seed set? I think not, but if so, can we check that packages do not save a random seed? Paul La version française suit le texte anglais. This email may contain privileged and/or confidential information, and the Bank of Canada does not waive any related rights. Any distribution, use, or copying of this email or the information it contains by other than the intended recipient is unauthorized. If you received this email in error please delete it immediately from your system and notify the sender promptly by email that you have done so. Le présent courriel peut contenir de l'information privilégiée ou confidentielle. La Banque du Canada ne renonce pas aux droits qui s'y rapportent. Toute diffusion, utilisation ou copie de ce courriel ou des renseignements qu'il contient par une personne autre que le ou les destinataires désignés est interdite. Si vous recevez ce courriel par erreur, veuillez le supprimer immédiatement et envoyer sans délai à l'expéditeur un message électronique pour l'aviser que vous avez éliminé de votre ordinateur toute copie du courriel reçu. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] FW: [R] same random numbers in different sessions
Dear Paul, On Tue, Oct 12, 2010 at 5:16 PM, Paul Gilbert wrote: > From R-help > ... >>I notice that you have the IPSUR package loaded; you know, just a >>shot in the dark here, but did you try not loading it? >> >>I ask because the vignette is built by making a special choice for >>set.seed, and the workspace that ships with the package might be >>interacting in an unexpected way. > > Is it possible that a package can save a set seed and have the effect that > users get when they save a workspace with the seed set? I think not, but if > so, can we check that packages do not save a random seed? > Yes, it is possible. For example, in principle, a person could include a workspace in the /data subdirectory of the package (which has had the seed set) and load the workspace when the package is loaded with the .First.lib function. That's not what I did, though, and it was not what I had in mind when I wrote that earlier reply to R-help. At that time I was worried that maybe I goofed and forgot to remove .Random.seed in the vignette, or something else was happening that I didn't understand. Turns out I didn't forget and everything is fine. Maybe somebody else could come up with a reason why a person would want the ability to load a .Random.seed with a package, though I don't have one off the top of my head. Regards, Jay *** G. Jay Kerns, Ph.D. Associate Professor Department of Mathematics & Statistics Youngstown State University Youngstown, OH 44555-0002 USA Office: 1035 Cushwa Hall Phone: (330) 941-3310 Office (voice mail) -3302 Department -3170 FAX VoIP: gjke...@ekiga.net E-mail: gke...@ysu.edu http://people.ysu.edu/~gkerns/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 'R CMD build' not cleaning the src/ folder on Windows
This problems seems to be solved in current R 2.12 RC. Thanks! H. On 10/10/2010 10:47 PM, Hervé Pagès wrote: Hi, 'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder on Windows: D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src BUS.cpp BUS.h D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS * checking for file 'meat\BUS/DESCRIPTION' ... OK * preparing 'BUS': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'BUS_1.5.0.tar.gz' D:\biocbld\bbs-2.7-bioc>tar ztvf BUS_1.5.0.tar.gz --wildcards '*.o' -rwxr--r-- biocbuild2/root 16503 2010-10-10 22:15 BUS/src/BUS.o Packages with a Makefile in src/ don't seem to be affected. This is with R 2.12.0 RC (2010-10-07 r53227). Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Wierd nlm behaviour in 2.10.1 and 2.12.0 [Sec=Unclassified]
Hi all,
When upgrading to 2.11.1 recently I noticed different results being produced by
my code.
After much digging I have finally narrowed it to a call to nlm().
This can be replicated by:
FixedRemovals<-1836180125888
AbStageInitial<-2223033830403
Rates<- 0.3102445
nlm(function(rootM,Abund,Loss,OtherM)
{(Loss-(rootM/(rootM+OtherM)*
(1-exp(-(rootM+OtherM)))*
Abund))^2}
,0.001,print.level=0,fscale=0, gradtol=1E-10, stepmax = 100.0
,Loss=FixedRemovals
,Abund=AbStageInitial
,OtherM=Rates)$estimate
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[Rd] Wierd nlm behaviour in 2.10.1 and 2.12.0 [Sec=Unclassified]
Hi all,
When upgrading to 2.11.1 recently I noticed different results being produced by
my code.
After MUCH digging into my code I have finally narrowed it to a call to nlm().
The problem actually occurs in 2.10.1 and 2.12.0.
This can be replicated by trying the code below in some different versions of R:
FixedRemovals<-1836180125888
AbStageInitial<-2223033830403
Rates<- 0.3102445
myfunc<-function(rootM,Abund,Loss,OtherM)
{(Loss-(rootM/(rootM+OtherM)*
(1-exp(-(rootM+OtherM)))*
Abund))^2}
nlm(myfunc
,0.001,print.level=0,fscale=0, gradtol=1E-10, stepmax = 100.0
,Loss=FixedRemovals
,Abund=AbStageInitial
,OtherM=Rates)
nlm(myfunc
,0.001,print.level=0,fscale=0, gradtol=1E-10, stepmax = 100.0
,Loss=FixedRemovals
,Abund=AbStageInitial
,OtherM=Rates)$estimate
Why would I be seeing a different value of 'estimate' (or any of the other
returned list items)?
Originally I thought it was 2.11.1 that was giving me the grief with different
output but now I see that in 2.11.1 I get the same value to each returned list
item both ways.
Can anyone explain this?
Thanks
Troy
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the
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in error,
please notify the sender immediately by e-mail or by telephoning +61 3 6232
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