Installing bioconductor from behind a firewall
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@michael-hoffman-882
Last seen 10.2 years ago
I have been trying to install Bioconductor on a HP alpha running OSF1 from behind a firewall that blocks outgoing port 80 and have had little success. We are required to use an HTTP proxy for all of our outgoing requests. Using getBioC() with method="wget" does not work because getBioC() tries to get many files using url() instead of download.file(), and so the specified method is not used. Is there an easy way to download the packages ahead of time and install them without needing an Internet connection during the install process? -- Michael Hoffman <hoffman@ebi.ac.uk> European Bioinformatics Institute
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@james-w-macdonald-5106
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You can download all the packages you are interested in at www.bioconductor.org, and then install using R CMD install. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Michael Hoffman <hoffman@ebi.ac.uk> 08/13/04 10:59AM >>> I have been trying to install Bioconductor on a HP alpha running OSF1 from behind a firewall that blocks outgoing port 80 and have had little success. We are required to use an HTTP proxy for all of our outgoing requests. Using getBioC() with method="wget" does not work because getBioC() tries to get many files using url() instead of download.file(), and so the specified method is not used. Is there an easy way to download the packages ahead of time and install them without needing an Internet connection during the install process? -- Michael Hoffman <hoffman@ebi.ac.uk> European Bioinformatics Institute _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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I've come across this problem in the past to install BioC in our linux cluster (in a private network). The best solution I found was mirroring the whole www.bioconductor.org web site with wget and changing the pointer for www.bioconductor.org to the internal mirrored server. Of course this is useful if what you want to install is most of the packages of BioC (as we did here). This way you don't have to worry about dependencies or other issues you might come across by scripting your own installation of BioC with "R CMD install". Hope this helps Jose On Mon, 2004-08-16 at 15:35, James MacDonald wrote: > You can download all the packages you are interested in at > www.bioconductor.org, and then install using R CMD install. > > Best, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> Michael Hoffman <hoffman@ebi.ac.uk> 08/13/04 10:59AM >>> > I have been trying to install Bioconductor on a HP alpha running OSF1 > from behind a firewall that blocks outgoing port 80 and have had > little success. We are required to use an HTTP proxy for all of our > outgoing requests. > > Using getBioC() with method="wget" does not work because getBioC() > tries to get many files using url() instead of download.file(), and so > the specified method is not used. > > Is there an easy way to download the packages ahead of time and > install them without needing an Internet connection during the install > process?
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> I've come across this problem in the past to install BioC in our linux > cluster (in a private network). The best solution I found was mirroring > the whole www.bioconductor.org web site with wget and changing the > pointer for www.bioconductor.org to the internal mirrored server. Yikes. I wish you had said something, as we probably could have found a much less painful solution. :) I just committed an updated version of reposTools (version 1.4.4), which I believe solves all of these issues. I'll wait a few days before moving these changes into the release branch, so it will be devel only until then (want to make extra sure that things are working properly before I do that, but the changes are important enough that they deserve to be in release, IMO). Thanks for pointing this out -J
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@michael-hoffman-882
Last seen 10.2 years ago
On Mon, 16 Aug 2004, James MacDonald wrote: > You can download all the packages you are interested in at > www.bioconductor.org, and then install using R CMD install. So I have to install them one by one this way? There's no distribution of them all? Thank you, -- Michael Hoffman <hoffman@ebi.ac.uk> European Bioinformatics Institute
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Dear Group, In the expression values, if there is N/A do we have to convert them to '0' before processing it? If so, how can I convert N/A to '0'? Thank you. PS --- Michael Hoffman <hoffman@ebi.ac.uk> wrote: > On Mon, 16 Aug 2004, James MacDonald wrote: > > > You can download all the packages you are > interested in at > > www.bioconductor.org, and then install using R CMD > install. > > So I have to install them one by one this way? > There's no distribution > of them all? > > Thank you, > -- > Michael Hoffman <hoffman@ebi.ac.uk> > European Bioinformatics Institute > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Please use an appropriate subject and not simply press reply to another thread. See the posting guide at the footnote. Please give more information about where does the missing value come from (flagging, failed spot criterion, computation) and what type of arrays (affy, cDNA) You do not necessarily zero impute for the following reasons : 1) There are other better ways of imputing. In the following papers, the authors showed that k-nn imputing is better than row mean and SVD imputation. Missing value estimation methods for DNA microarrays. Troyanskaya O., Cantor M., Sherlock G., Brown P., Hastie T., Tibshirani R., Botstein D., Altman R.B. Bioinformatics 2001; 17(6):520-5 PMID:11395428 There are more recent papers on missing value imputation for microarrays. Try a google or pubmed search and you will find many more. 2) Most of the functions in R can deal with missing values if you set the argument na.rm = TRUE. Some do this by default (see below) or you can easily write a parser. t.test( c(500,502,501, NA, NA), c(400,380,410, NA) )$p.value [1] 0.006880871 t.test( c(500,502,501, 0, 0), c(400,380,410, 0) )$p.value [1] 0.9848868 This example also shows you an example when some imputation can be inappropriate. 3) Missing values can be informative but this depends on how the missing values were generated. I commonly filter genes with more than 70% missing (across arrays) to avoid spurious results. Sometimes arrays with more than say 50% missing value can be indicative of array problems. In short, this is depends on how much missing values you have, if they are informative and what do you want to use them for. I tend to impute the data only if I plan on using some classification method that cannot handle missing values. Regards, Adai. On Tue, 2004-08-17 at 13:48, S Peri wrote: > Dear Group, > In the expression values, if there is N/A do we have > to convert them to '0' before processing it? > If so, how can I convert N/A to '0'? > > Thank you. > PS > > > > --- Michael Hoffman <hoffman@ebi.ac.uk> wrote: > > > On Mon, 16 Aug 2004, James MacDonald wrote: > > > > > You can download all the packages you are > > interested in at > > > www.bioconductor.org, and then install using R CMD > > install. > > > > So I have to install them one by one this way? > > There's no distribution > > of them all? > > > > Thank you, > > -- > > Michael Hoffman <hoffman@ebi.ac.uk> > > European Bioinformatics Institute > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Thank you for your suggestions Adai. I am sorry for being ignorant about the subject thread. I will take care of that from now. regards, PS --- Adaikalavan Ramasamy <ramasamy@cancer.org.uk> wrote: > Please use an appropriate subject and not simply > press reply to another > thread. See the posting guide at the footnote. > > Please give more information about where does the > missing value come > from (flagging, failed spot criterion, computation) > and what type of > arrays (affy, cDNA) > > You do not necessarily zero impute for the following > reasons : > > > 1) There are other better ways of imputing. In the > following papers, the > authors showed that k-nn imputing is better than row > mean and SVD > imputation. > > Missing value estimation methods for DNA > microarrays. > Troyanskaya O., Cantor M., Sherlock G., Brown P., > Hastie T., Tibshirani > R., Botstein D., Altman R.B. > Bioinformatics 2001; 17(6):520-5 > PMID:11395428 > > There are more recent papers on missing value > imputation for > microarrays. Try a google or pubmed search and you > will find many more. > > > 2) Most of the functions in R can deal with missing > values if you set > the argument na.rm = TRUE. Some do this by default > (see below) or you > can easily write a parser. > > t.test( c(500,502,501, NA, NA), c(400,380,410, NA) > )$p.value > [1] 0.006880871 > > t.test( c(500,502,501, 0, 0), c(400,380,410, 0) > )$p.value > [1] 0.9848868 > > This example also shows you an example when some > imputation can be > inappropriate. > > > 3) Missing values can be informative but this > depends on how the missing > values were generated. I commonly filter genes with > more than 70% > missing (across arrays) to avoid spurious results. > Sometimes arrays with > more than say 50% missing value can be indicative of > array problems. > > > In short, this is depends on how much missing values > you have, if they > are informative and what do you want to use them > for. I tend to impute > the data only if I plan on using some classification > method that cannot > handle missing values. > > > Regards, Adai. > > > On Tue, 2004-08-17 at 13:48, S Peri wrote: > > Dear Group, > > In the expression values, if there is N/A do we > have > > to convert them to '0' before processing it? > > If so, how can I convert N/A to '0'? > > > > Thank you. > > PS > > > > > > > > --- Michael Hoffman <hoffman@ebi.ac.uk> wrote: > > > > > On Mon, 16 Aug 2004, James MacDonald wrote: > > > > > > > You can download all the packages you are > > > interested in at > > > > www.bioconductor.org, and then install using R > CMD > > > install. > > > > > > So I have to install them one by one this way? > > > There's no distribution > > > of them all? > > > > > > Thank you, > > > -- > > > Michael Hoffman <hoffman@ebi.ac.uk> > > > European Bioinformatics Institute > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >
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