siggenes 1.10 na.handling

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He, Yiwen NIH/CIT ▴ 360

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ADD COMMENT • link updated 17.6 years ago by Seth Falcon ★ 7.4k • written 17.6 years ago by He, Yiwen NIH/CIT ▴ 360

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Seth Falcon ★ 7.4k

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"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Yiwen, > > He, Yiwen (NIH/CIT) [C] wrote: >> Hi Mr. Schwender and others, >> >> >> >> I've been using the na.handling function in siggenes, which becomes an >> internal function in the latest version siggenes 1.10 (BioC 2.0). Can >> anyone tell me how I can still make use of this internal function in the >> new version? > > This all depends on how you plan to make use of the function. If you are > using it in a package that has a NAMESPACE, you can just add siggenes to > your imports list, or just import that function using the importFrom > directive. See 'Writing R Extensions', in particular the section > 'Package Name Spaces'. > > If you are using the function interactively, then you can use the triple > colon operator ':::' (e.g., siggenes:::na.handler(args)). If a function is not exported from a package, then it is _only_ accessible using ':::'. You cannot import a non-exported function, etc. If this is a function you use, I would recommend contacting the siggenes maintainer and asking if it would be possible to export this function. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

ADD COMMENT • link 17.6 years ago Seth Falcon ★ 7.4k

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Hi Yiwen, I have updated siggenes in both the devel and the release branch. (I hope that it is okay that I also have updated this at the release branch.) If you install siggenes version 1.10.1 (release) or 1.11.4 (devel) you should be able to use na.handling without the :::. These versions should be available at Bioconductor soon. But please consider that na.handling only provides adhoc methods for implementing missing values, and that there are better imputation methods than just using the mean or median. Best, Holger -------- Original-Nachricht -------- Datum: Wed, 23 May 2007 12:51:37 -0700 Von: Seth Falcon <sfalcon at="" fhcrc.org=""> An: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> CC: "He, Yiwen \\(NIH/CIT\\) \\[C\\]" <heyiwen at="" mail.nih.gov="">, bioconductor at stat.math.ethz.ch Betreff: Re: [BioC] siggenes 1.10 na.handling > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > > > Hi Yiwen, > > > > He, Yiwen (NIH/CIT) [C] wrote: > >> Hi Mr. Schwender and others, > >> > >> > >> > >> I've been using the na.handling function in siggenes, which becomes an > >> internal function in the latest version siggenes 1.10 (BioC 2.0). Can > >> anyone tell me how I can still make use of this internal function in > the > >> new version? > > > > This all depends on how you plan to make use of the function. If you are > > using it in a package that has a NAMESPACE, you can just add siggenes to > > your imports list, or just import that function using the importFrom > > directive. See 'Writing R Extensions', in particular the section > > 'Package Name Spaces'. > > > > If you are using the function interactively, then you can use the triple > > colon operator ':::' (e.g., siggenes:::na.handler(args)). > > If a function is not exported from a package, then it is _only_ > accessible using ':::'. You cannot import a non-exported function, > etc. > > If this is a function you use, I would recommend contacting the > siggenes maintainer and asking if it would be possible to export this > function. > > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research > Center > http://bioconductor.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail

ADD REPLY • link 17.6 years ago Holger Schwender ▴ 900

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James W. MacDonald 67k

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Hi Yiwen, He, Yiwen (NIH/CIT) [C] wrote: > Hi Mr. Schwender and others, > > > > I've been using the na.handling function in siggenes, which becomes an > internal function in the latest version siggenes 1.10 (BioC 2.0). Can > anyone tell me how I can still make use of this internal function in the > new version? This all depends on how you plan to make use of the function. If you are using it in a package that has a NAMESPACE, you can just add siggenes to your imports list, or just import that function using the importFrom directive. See 'Writing R Extensions', in particular the section 'Package Name Spaces'. If you are using the function interactively, then you can use the triple colon operator ':::' (e.g., siggenes:::na.handler(args)). Best, Jim > > > > Thanks a lot, > > > > Yiwen He > > BIMAS/DCB/CIT/NIH > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD COMMENT • link 17.6 years ago James W. MacDonald 67k

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