Need help finding "aroma" package for R2.9

0

Entering edit mode

Ochsner, Scott A ▴ 60

@ochsner-scott-a-4334

Last seen 9.7 years ago

Hello, I'm trying to repeat an old two-color array analysis published in 2008 which used R2.9. The authors used the "kth" package which depends on the "aroma" package. Can anyone point me to a directory where I might find the "aroma" package suitable for use with R2.9. I've tried to use "aroma.core" without success. The "kth" package, not surprisingly, would not recognize "aroma.core". > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.18.3 annotate_1.22.0 AnnotationDbi_1.6.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] DBI_0.2-5 RSQLite_0.8-2 tools_2.9.0 xtable_1.5-6 Thanks for any help, Scott Scott A. Ochsner, PhD NURSA Bioinformatics Baylor College of Medicine One Baylor Plaza Mail Stop: BCM-130 Houston, TX 77030 Voice: (713) 798-6227 Fax: (713) 790-1275

• 884 views

ADD COMMENT • link updated 13.2 years ago by Steve Lianoglou ★ 13k • written 13.2 years ago by Ochsner, Scott A ▴ 60

0

Entering edit mode

Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 14 months ago

United States

Hi, On Fri, Feb 25, 2011 at 11:24 AM, Ochsner, Scott A <sochsner at="" bcm.edu=""> wrote: > Hello, > > I'm trying to repeat an old two-color array analysis published in 2008 which used R2.9. ?The authors used the "kth" package which depends on the "aroma" package. ?Can anyone point me to a directory where I might find the "aroma" package suitable for use with R2.9. ?I've tried to use "aroma.core" without success. ?The "kth" package, not surprisingly, would not recognize "aroma.core". I think you'll want to start your search here: http://www.aroma-project.org/ Although, the lead developer for the aroma project is also on this list, so perhaps he'll have some more useful tips for you. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 13.2 years ago Steve Lianoglou ★ 13k

0

Entering edit mode

Hello again, Just to follow up: thanks to a lead from Steve I was able to track down archived versions of the aroma package and its various dependencies at http://www.braju.com/R/repos/ Scott Scott A. Ochsner, PhD One Baylor Plaza BCM130, Houston, TX 77030 Voice: (713) 798-6227 Fax: (713) 790-1275 -----Original Message----- From: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Sent: Friday, February 25, 2011 10:33 AM To: Ochsner, Scott A Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Need help finding "aroma" package for R2.9 Hi, On Fri, Feb 25, 2011 at 11:24 AM, Ochsner, Scott A <sochsner at="" bcm.edu=""> wrote: > Hello, > > I'm trying to repeat an old two-color array analysis published in 2008 which used R2.9. ?The authors used the "kth" package which depends on the "aroma" package. ?Can anyone point me to a directory where I might find the "aroma" package suitable for use with R2.9. ?I've tried to use "aroma.core" without success. ?The "kth" package, not surprisingly, would not recognize "aroma.core". I think you'll want to start your search here: http://www.aroma-project.org/ Although, the lead developer for the aroma project is also on this list, so perhaps he'll have some more useful tips for you. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 13.2 years ago Ochsner, Scott A ▴ 60

0

Entering edit mode

Hi, sorry for the delay. I've just added a page to the Aroma Project website http://www.aroma-project.org/packages/aroma/ which shows to install the "original" aroma package (extending the sma package), which, despite it's name is quite different from all other packages (aroma.affymetrix, aroma.cn, aroma.core, ...) on the Aroma Project website. /Henrik PS. Your manual installation approach would work as well. On Fri, Feb 25, 2011 at 12:07 PM, Ochsner, Scott A <sochsner at="" bcm.edu=""> wrote: > ?Hello again, > > Just to follow up: ?thanks to a lead from Steve I was able to track down archived versions of the aroma package and its various dependencies at http://www.braju.com/R/repos/ > > Scott > > > Scott A. Ochsner, PhD > One Baylor Plaza BCM130, Houston, TX 77030 > Voice: (713) 798-6227 ?Fax: (713) 790-1275 > -----Original Message----- > From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] > Sent: Friday, February 25, 2011 10:33 AM > To: Ochsner, Scott A > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Need help finding "aroma" package for R2.9 > > Hi, > > On Fri, Feb 25, 2011 at 11:24 AM, Ochsner, Scott A <sochsner at="" bcm.edu=""> wrote: >> Hello, >> >> I'm trying to repeat an old two-color array analysis published in 2008 which used R2.9. ?The authors used the "kth" package which depends on the "aroma" package. ?Can anyone point me to a directory where I might find the "aroma" package suitable for use with R2.9. ?I've tried to use "aroma.core" without success. ?The "kth" package, not surprisingly, would not recognize "aroma.core". > > I think you'll want to start your search here: > > http://www.aroma-project.org/ > > Although, the lead developer for the aroma project is also on this > list, so perhaps he'll have some more useful tips for you. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD REPLY • link 13.2 years ago Henrik Bengtsson ★ 2.4k

Login before adding your answer.