exonmap install
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Dick Beyer ★ 1.4k
@dick-beyer-26
Last seen 9.6 years ago
Has anyone done the complete install of the mysql Ensembl databases that are used by the exonmap package? The sizes of some of the database dumps at ftp://ftp.ensembl.org/pub/ are pretty daunting. I am using the affy mouse exon arrays and wondered if, initially at least, I could just install some smaller portion of all the recommended data in order to do a gene core analysis? That is, could I just install, say, the files from: ftp://ftp.ensembl.org/pub/current_mus_musculus/data/mysql/mus_musculus _core_43_36d rather than of the files from current_mus_musculus? And could I delay installing the "Multi-species data" and the "BioMart data"? Or do the commands I would use to get a core gene list from the exon CEL files need to access all those database tables? Thanks much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer
affy exonmap affy exonmap • 1.3k views
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@james-w-macdonald-5106
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Hi Dick, Dick Beyer wrote: > Has anyone done the complete install of the mysql Ensembl databases > that are used by the exonmap package? The sizes of some of the > database dumps at ftp://ftp.ensembl.org/pub/ are pretty daunting. > > I am using the affy mouse exon arrays and wondered if, initially at > least, I could just install some smaller portion of all the > recommended data in order to do a gene core analysis? That is, could > I just install, say, the files from: > > ftp://ftp.ensembl.org/pub/current_mus_musculus/data/mysql/mus_muscul us_core_43_36d I have installed the xmap stuff for the human exon arrays, and all I needed were the homo_sapiens_core_43_36d files. Does the INSTALL.TXT that comes with the mouse version differ in what they say you need to download? Naively I would assume what you need would be the same (only mouse, not human). As an aside, I have some functions I wrote to do what I think is a more reasonable analysis of these data than simply doing loads of t-tests for each probeset. If you are interested I can send them to you. I would be interested in any feedback you might have. Note that these are bare functions, not a package, and I just started writing them this week so they are in super-pre-alpha status ;-D. Best, Jim > > > rather than of the files from current_mus_musculus? And could I > delay installing the "Multi-species data" and the "BioMart data"? Or > do the commands I would use to get a core gene list from the exon CEL > files need to access all those database tables? > > Thanks much, Dick > ******************************************************************** *********** > Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 > Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 > Roosevelt Way NE, # 100 Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > > _______________________________________________ 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.
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Hi Jim, Thanks for letting me know you were successful with just the homo_sapiens_core_43_36d dataset. I will try that with the mouse. And I would love to take you up on your kind offer to try your new functions. Using super-pre-alpha makes me feel alive :-) Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Fri, 23 Mar 2007, James W. MacDonald wrote: > Hi Dick, > > Dick Beyer wrote: >> Has anyone done the complete install of the mysql Ensembl databases >> that are used by the exonmap package? The sizes of some of the >> database dumps at ftp://ftp.ensembl.org/pub/ are pretty daunting. >> >> I am using the affy mouse exon arrays and wondered if, initially at >> least, I could just install some smaller portion of all the >> recommended data in order to do a gene core analysis? That is, could >> I just install, say, the files from: >> >> ftp://ftp.ensembl.org/pub/current_mus_musculus/data/mysql/mus_muscu lus_core_43_36d > > I have installed the xmap stuff for the human exon arrays, and all I needed > were the homo_sapiens_core_43_36d files. Does the INSTALL.TXT that comes with > the mouse version differ in what they say you need to download? Naively I would > assume what you need would be the same (only mouse, not human). > > As an aside, I have some functions I wrote to do what I think is a more > reasonable analysis of these data than simply doing loads of t-tests for each > probeset. If you are interested I can send them to you. I would be interested > in any feedback you might have. > > Note that these are bare functions, not a package, and I just started writing > them this week so they are in super-pre-alpha status ;-D. > > Best, > > Jim > > >> >> >> rather than of the files from current_mus_musculus? And could I >> delay installing the "Multi-species data" and the "BioMart data"? Or >> do the commands I would use to get a core gene list from the exon CEL >> files need to access all those database tables? >> >> Thanks much, Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 >> Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 >> Roosevelt Way NE, # 100 Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> >> _______________________________________________ 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. >
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Dick, Jim, As for installing local Ensembl: some of the tables in Ensembl installations are not needed in exonmap but we cannot guarantee, that they will not be used in future versions. And 16G of data fits with no problem to a normal hard disc capacity, so it seems easier to download it as a whole, than to choose appropriate tables. The idea of exonmap was mainly to process gene-transcript-exon-probeset-genome annotations, but in includes bits of analysis, too. Recently, from the version 0.1.7 in addition to the pairwise comparison, there are functions for high-throughput alternative splicing searches, according to what's in Affy white papers: splicing.index() and splanova() for MIDAS-like splicing ANOVA in the case of multiple treatments. There was also added the most fancy, heatmap-like plot for multiexonic genes so far: gene.strip() Cheers, Michal -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer Sent: 23 March 2007 20:02 To: James W. MacDonald Cc: Bioconductor Subject: Re: [BioC] exonmap install Hi Jim, Thanks for letting me know you were successful with just the homo_sapiens_core_43_36d dataset. I will try that with the mouse. And I would love to take you up on your kind offer to try your new functions. Using super-pre-alpha makes me feel alive :-) Cheers, Dick ********************************************************************** ** ******* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ** ******* On Fri, 23 Mar 2007, James W. MacDonald wrote: > Hi Dick, > > Dick Beyer wrote: >> Has anyone done the complete install of the mysql Ensembl databases >> that are used by the exonmap package? The sizes of some of the >> database dumps at ftp://ftp.ensembl.org/pub/ are pretty daunting. >> >> I am using the affy mouse exon arrays and wondered if, initially at >> least, I could just install some smaller portion of all the >> recommended data in order to do a gene core analysis? That is, could >> I just install, say, the files from: >> >> ftp://ftp.ensembl.org/pub/current_mus_musculus/data/mysql/mus_musculu >> s_core_43_36d > > I have installed the xmap stuff for the human exon arrays, and all I > needed were the homo_sapiens_core_43_36d files. Does the INSTALL.TXT > that comes with the mouse version differ in what they say you need to > download? Naively I would assume what you need would be the same (only mouse, not human). > > As an aside, I have some functions I wrote to do what I think is a > more reasonable analysis of these data than simply doing loads of > t-tests for each probeset. If you are interested I can send them to > you. I would be interested in any feedback you might have. > > Note that these are bare functions, not a package, and I just started > writing them this week so they are in super-pre-alpha status ;-D. > > Best, > > Jim > > >> >> >> rather than of the files from current_mus_musculus? And could I >> delay installing the "Multi-species data" and the "BioMart data"? Or >> do the commands I would use to get a core gene list from the exon CEL >> files need to access all those database tables? >> >> Thanks much, Dick >> ********************************************************************** ** ******* >> Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 >> Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 >> Roosevelt Way NE, # 100 Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> >> _______________________________________________ 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. > _______________________________________________ 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 -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Hi Michal, Michal Okoniewski wrote: > Dick, Jim, > > As for installing local Ensembl: some of the tables in Ensembl > installations are not > needed in exonmap but we cannot guarantee, that they will not be used in > future > versions. And 16G of data fits with no problem to a normal hard disc > capacity, so it > seems easier to download it as a whole, than to choose appropriate > tables. This just includes the e.g., mus_musculus_core_41_36b files, correct? In other words, if one downloads all the files in that directory and installs that should be sufficient. Best, Jim > > > The idea of exonmap was mainly to process > gene-transcript-exon-probeset-genome > annotations, but in includes bits of analysis, too. > Recently, from the version 0.1.7 in addition to the pairwise comparison, > there are > functions for high-throughput alternative splicing searches, > according to what's in Affy white papers: splicing.index() > and splanova() for MIDAS-like splicing ANOVA in the case of multiple > treatments. There was also added the most fancy, heatmap-like plot for > multiexonic > genes so far: gene.strip() > > Cheers, > Michal > -- 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.
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Hi Jim and Michal, I made the mistake of using the xmap_mus_musculus_core_41_36b mysql files with the Ensembl mus_musculus_core_43_36d mysql data. The exonmap and Jim's exonModel routines work great when I used both xmap_mus_musculus_core_41_36b files and mus_musculus_core_41_36b data. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Mon, 26 Mar 2007, James W. MacDonald wrote: > Hi Michal, > > Michal Okoniewski wrote: >> Dick, Jim, As for installing local Ensembl: some of the tables in Ensembl >> installations are not >> needed in exonmap but we cannot guarantee, that they will not be used in >> future versions. And 16G of data fits with no problem to a normal hard disc >> capacity, so it seems easier to download it as a whole, than to choose >> appropriate >> tables. > > This just includes the e.g., mus_musculus_core_41_36b files, correct? In other > words, if one downloads all the files in that directory and installs that > should be sufficient. > > Best, > > Jim > > >> >> >> The idea of exonmap was mainly to process >> gene-transcript-exon-probeset-genome annotations, but in includes bits of >> analysis, too. Recently, from the version 0.1.7 in addition to the pairwise >> comparison, >> there are functions for high-throughput alternative splicing searches, >> according to what's in Affy white papers: splicing.index() >> and splanova() for MIDAS-like splicing ANOVA in the case of multiple >> treatments. There was also added the most fancy, heatmap-like plot for >> multiexonic genes so far: gene.strip() >> >> Cheers, Michal > > -- > 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. >
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Hi Jim, I am also working on Affy human all exon array data, could you also send your functions to me? Best, Shirley On 3/23/07, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Dick, > > Dick Beyer wrote: > > Has anyone done the complete install of the mysql Ensembl databases > > that are used by the exonmap package? The sizes of some of the > > database dumps at ftp://ftp.ensembl.org/pub/ are pretty daunting. > > > > I am using the affy mouse exon arrays and wondered if, initially at > > least, I could just install some smaller portion of all the > > recommended data in order to do a gene core analysis? That is, could > > I just install, say, the files from: > > > > ftp://ftp.ensembl.org/pub/current_mus_musculus/data/mysql/mus_musc ulus_core_43_36d > > I have installed the xmap stuff for the human exon arrays, and all I > needed were the homo_sapiens_core_43_36d files. Does the INSTALL.TXT > that comes with the mouse version differ in what they say you need to > download? Naively I would assume what you need would be the same (only > mouse, not human). > > As an aside, I have some functions I wrote to do what I think is a more > reasonable analysis of these data than simply doing loads of t-tests for > each probeset. If you are interested I can send them to you. I would be > interested in any feedback you might have. > > Note that these are bare functions, not a package, and I just started > writing them this week so they are in super-pre-alpha status ;-D. > > Best, > > Jim > > > > > > > > rather than of the files from current_mus_musculus? And could I > > delay installing the "Multi-species data" and the "BioMart data"? Or > > do the commands I would use to get a core gene list from the exon CEL > > files need to access all those database tables? > > > > Thanks much, Dick > > ****************************************************************** ************* > > Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 > > Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 > > Roosevelt Way NE, # 100 Seattle, WA 98105-6099 > > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > > http://staff.washington.edu/~dbeyer > > > > _______________________________________________ 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. > > _______________________________________________ > 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 >
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