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Question: Packages "clusterProfiler" and "illuminaHumanv4.db" not available for installation
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gravatar for Luke Pilling
6.5 years ago by
Luke Pilling10
Luke Pilling10 wrote:
Hello, and thanks for your time. I am new to Bioconductor, and cannot seem to get off the starting line as yet. I have so far successfully installed several useful packages into my R installation (v2.10.1). However, I have Illumina HT12 microarray data, and have thus tried to install "illuminaHumanv4.db" (annotation file) to accompany the annotation tools I have also downloaded, but it is apparently unavailable when I run the command 'biocLite("illuminaHumanv4.db")'. The same is also true for "clusterProfiler" - it would be a great tool to use, however it is also unavailable using the appropriate command. I am using a Windows machine, and both packages are apparently compliant with a Windows installation. I do not have access to a linux machine in this office. Is this a common issue, and will they become available again? And if not, how would I go about manually installing the packages from the available downloads? Many thanks, Luke Pilling ---- Luke Pilling Associate Research Fellow Epidemiology and Public Health Peninsula Medical School, Barrack Road, Exeter, EX2 5DW, U.K. [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.5 years ago by Steve Lianoglou12k • written 6.5 years ago by Luke Pilling10
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gravatar for Steve Lianoglou
6.5 years ago by
Genentech
Steve Lianoglou12k wrote:
Hi, On Tue, May 31, 2011 at 8:01 AM, Luke Pilling <luke.pilling at="" pcmd.ac.uk=""> wrote: > Hello, and thanks for your time. > > I am new to Bioconductor, and cannot seem to get off the starting line as yet. I have so far successfully installed several useful packages into my R installation (v2.10.1). > > However, I have Illumina HT12 microarray data, and have thus tried to install "illuminaHumanv4.db" (annotation file) to accompany the annotation tools I have also downloaded, but it is apparently unavailable when I run the command 'biocLite("illuminaHumanv4.db")'. > > The same is also true for "clusterProfiler" - it would be a great tool to use, however it is also unavailable using the appropriate command. > > I am using a Windows machine, and both packages are apparently compliant with a Windows installation. I do not have access to a linux machine in this office. > > Is this a common issue, and will they become available again? And if not, how would I go about manually installing the packages from the available downloads? The likely problem is that you are using a (very) old version of R, which in turn is using an older version of bioconductor. Please install the newest version of R (2.13) and then reinstall your bioconductor packages via the biocLite mechanism. HTH, -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 COMMENTlink written 6.5 years ago by Steve Lianoglou12k
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