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Question: DEseq version and R version compatibility
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6.0 years ago by
José Luis Lavín270 wrote:
Dear all, First of all I'd like to apologize for bothering you with such a naive question, but I've been told that this is the place to ask about this particular issue. I'm trying to perform a Differential Expresion analysis on some RNA- seq experiments using DEseq package. I'm not very fluent with R yet, and I'm facing some problems while using DEseq for the analysis. In my institution the R version of the Linux servers system is 2.13.0 and the version I installed in my windows terminal is 2.15.2. I've retrieved multiple DEseq manual versions from the internet (dated 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one to another and some are not supported in one or the other R versions I have available. I need the R script to work in both versions and I don't really know how to achieve it... Could you please help me solving this giving me some kind of advice on how to get a functional and compatible script to be used with both R versions I previously stated? Thanks in advance for your kind support. With best wishes JL -- -- Dr. José Luis Lavín Trueba Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN [[alternative HTML version deleted]]
ADD COMMENTlink
modified 6.0 years ago by Thomas Girke1.6k • written 6.0 years ago by José Luis Lavín270
0
6.0 years ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:
There is no good reason not to keep R and Bioc fully up-to-date on a Linux server for all users while maintaining older versions too. If they have certain dependencies then one can easily configure things that users can call a specific R version by its version number, e.g. calling the latest version by typing R-2.15.2 instead of just R. A more generic solution to this is usually to use a module system that administers versions of any software not just R: http://modules.sourceforge.net/. This can be extremely useful in the NGS analysis world since you will end up installing new versions of all kinds of software (e.g. aligners, assemblers, Perl/Python modules) almost every day. Thomas On Thu, Oct 04, 2012 at 12:24:46PM +0000, Jos? Luis Lav?n wrote: > Dear all, > > First of all I'd like to apologize for bothering you with such a naive > question, but I've been told that this is the place to ask about this > particular issue. > > I'm trying to perform a Differential Expresion analysis on some RNA- seq > experiments using DEseq package. I'm not very fluent with R yet, and I'm > facing some problems while using DEseq for the analysis. In my institution > the R version of the Linux servers system is 2.13.0 and the version I > installed in my windows terminal is 2.15.2. > I've retrieved multiple DEseq manual versions from the internet (dated > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one > to another and some are not supported in one or the other R versions I have > available. I need the R script to work in both versions and I don't really > know how to achieve it... > Could you please help me solving this giving me some kind of advice on how > to get a functional and compatible script to be used with both R versions I > previously stated? > > Thanks in advance for your kind support. > > With best wishes > > JL > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 COMMENTlink written 6.0 years ago by Thomas Girke1.6k
Dear Jose Luis please either convince your sys admin to install the current release version of R (2.15.1) and Bioconductor (2.11), or install it privately on the server e.g. in your home directory (it is easy). Everything else leads to insanity. Note that each R package (incl. DESeq) comes with its documentation, and it is versioned by a version number rather than calendar dates. The presence of outdated PDFs somewhere in the internet does not mean that you should these. Best wishes Wolfgang Il giorno Oct 4, 2012, alle ore 4:41 PM, Thomas Girke <thomas.girke at="" ucr.edu=""> ha scritto: > > There is no good reason not to keep R and Bioc fully up-to-date on a > Linux server for all users while maintaining older versions too. If they > have certain dependencies then one can easily configure things that > users can call a specific R version by its version number, e.g. calling > the latest version by typing R-2.15.2 instead of just R. A more generic > solution to this is usually to use a module system that administers > versions of any software not just R: http://modules.sourceforge.net/. > This can be extremely useful in the NGS analysis world since you will > end up installing new versions of all kinds of software (e.g. aligners, > assemblers, Perl/Python modules) almost every day. > > Thomas > > > On Thu, Oct 04, 2012 at 12:24:46PM +0000, Jos? Luis Lav?n wrote: >> Dear all, >> >> First of all I'd like to apologize for bothering you with such a naive >> question, but I've been told that this is the place to ask about this >> particular issue. >> >> I'm trying to perform a Differential Expresion analysis on some RNA-seq >> experiments using DEseq package. I'm not very fluent with R yet, and I'm >> facing some problems while using DEseq for the analysis. In my institution >> the R version of the Linux servers system is 2.13.0 and the version I >> installed in my windows terminal is 2.15.2. >> I've retrieved multiple DEseq manual versions from the internet (dated >> 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one >> to another and some are not supported in one or the other R versions I have >> available. I need the R script to work in both versions and I don't really >> know how to achieve it... >> Could you please help me solving this giving me some kind of advice on how >> to get a functional and compatible script to be used with both R versions I >> previously stated? >> >> Thanks in advance for your kind support. >> >> With best wishes >> >> JL >> >> -- >> -- >> Dr. Jos? Luis Lav?n Trueba >> >> Dpto. de Producci?n Agraria >> Grupo de Gen?tica y Microbiolog?a >> Universidad P?blica de Navarra >> 31006 Pamplona >> Navarra >> SPAIN >> >> [[alternative HTML version deleted]] >> > >> _______________________________________________ >> 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 > > _______________________________________________ > 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 REPLYlink written 6.0 years ago by Wolfgang Huber13k
0
6.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Thu, Oct 4, 2012 at 8:24 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: > Dear all, > > First of all I'd like to apologize for bothering you with such a naive > question, but I've been told that this is the place to ask about this > particular issue. > > I'm trying to perform a Differential Expresion analysis on some RNA- seq > experiments using DEseq package. I'm not very fluent with R yet, and I'm > facing some problems while using DEseq for the analysis. In my institution > the R version of the Linux servers system is 2.13.0 and the version I > installed in my windows terminal is 2.15.2. > I've retrieved multiple DEseq manual versions from the internet (dated > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one > to another and some are not supported in one or the other R versions I have > available. I need the R script to work in both versions and I don't really > know how to achieve it... > Could you please help me solving this giving me some kind of advice on how > to get a functional and compatible script to be used with both R versions I > previously stated? Hi, Jos?. The versions of DEseq are matched to the versions of bioconductor which are matched to the versions of R. In other words, the only way to match the versions of DEseq between two machines is to use the same version of R on both. Installing R in your home directory is not difficult, so I'd suggest you try that on your linux cluster since R-2.13 is pretty outdated at this point. Also, you'll want to ALWAYS use biocLite() to install packages, as detailed on the bioconductor website. This can avoid headaches with version mismatches in the future. Sean > Thanks in advance for your kind support. > > With best wishes > > JL > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 COMMENTlink written 6.0 years ago by Sean Davis21k
Hello Sean, The main problem with updating the R version of the servers is that I'm not the SysAdmin, and he told me that they couldn't update it at the moment because they have some processes and pipelines that need the old R version (2.13), so he can't update it (weird, isn't it?). That's why I was looking for such strange compatibility... Anyway, due to my current low level on R scripting, when I come across a command that isn't functional I don't really know what to do but trying to use another manual version hoping the code there will fix it...but I've had no luck with that at the moment. That's why I asked about this. I'll keep trying to make DEseq work, but I begin to feel stupid, reading everybody seems to be able to run it except myself. Thank you for your swift answer, anyway Best wishes JL 2012/10/4 Sean Davis <sdavis2@mail.nih.gov> > On Thu, Oct 4, 2012 at 8:24 AM, José Luis Lavín <jluis.lavin@unavarra.es> > wrote: > > Dear all, > > > > First of all I'd like to apologize for bothering you with such a naive > > question, but I've been told that this is the place to ask about this > > particular issue. > > > > I'm trying to perform a Differential Expresion analysis on some RNA-seq > > experiments using DEseq package. I'm not very fluent with R yet, and I'm > > facing some problems while using DEseq for the analysis. In my > institution > > the R version of the Linux servers system is 2.13.0 and the version I > > installed in my windows terminal is 2.15.2. > > I've retrieved multiple DEseq manual versions from the internet (dated > > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from > one > > to another and some are not supported in one or the other R versions I > have > > available. I need the R script to work in both versions and I don't > really > > know how to achieve it... > > Could you please help me solving this giving me some kind of advice on > how > > to get a functional and compatible script to be used with both R > versions I > > previously stated? > > Hi, José. > > The versions of DEseq are matched to the versions of bioconductor > which are matched to the versions of R. In other words, the only way > to match the versions of DEseq between two machines is to use the same > version of R on both. Installing R in your home directory is not > difficult, so I'd suggest you try that on your linux cluster since > R-2.13 is pretty outdated at this point. > > Also, you'll want to ALWAYS use biocLite() to install packages, as > detailed on the bioconductor website. This can avoid headaches with > version mismatches in the future. > > Sean > > > > Thanks in advance for your kind support. > > > > With best wishes > > > > JL > > > > -- > > -- > > Dr. José Luis Lavín Trueba > > > > Dpto. de Producción Agraria > > Grupo de Genética y Microbiología > > Universidad Pública de Navarra > > 31006 Pamplona > > Navarra > > SPAIN > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- -- Dr. José Luis Lavín Trueba Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by José Luis Lavín270
On Thu, Oct 4, 2012 at 9:30 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: > Hello Sean, > > The main problem with updating the R version of the servers is that I'm not > the SysAdmin, and he told me that they couldn't update it at the moment > because they have some processes and pipelines that need the old R version > (2.13), so he can't update it (weird, isn't it?). That's why I was looking > for such strange compatibility... > Anyway, due to my current low level on R scripting, when I come across a > command that isn't functional I don't really know what to do but trying to > use another manual version hoping the code there will fix it...but I've had > no luck with that at the moment. That's why I asked about this. > I'll keep trying to make DEseq work, but I begin to feel stupid, reading > everybody seems to be able to run it except myself. If you have a good relationship with your sysadmin, ask him/her to help you to install R in your home directory. This is not hard to do (hopefully, for a sysadmin) and will allow you to run a different version of R than that already installed on the system. Really, doing this will be much better than copying code from various versions of packages to "just make it work". Sean > Thank you for your swift answer, anyway > > Best wishes > > JL > > 2012/10/4 Sean Davis <sdavis2 at="" mail.nih.gov=""> > >> On Thu, Oct 4, 2012 at 8:24 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> >> wrote: >> > Dear all, >> > >> > First of all I'd like to apologize for bothering you with such a naive >> > question, but I've been told that this is the place to ask about this >> > particular issue. >> > >> > I'm trying to perform a Differential Expresion analysis on some RNA-seq >> > experiments using DEseq package. I'm not very fluent with R yet, and I'm >> > facing some problems while using DEseq for the analysis. In my >> institution >> > the R version of the Linux servers system is 2.13.0 and the version I >> > installed in my windows terminal is 2.15.2. >> > I've retrieved multiple DEseq manual versions from the internet (dated >> > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from >> one >> > to another and some are not supported in one or the other R versions I >> have >> > available. I need the R script to work in both versions and I don't >> really >> > know how to achieve it... >> > Could you please help me solving this giving me some kind of advice on >> how >> > to get a functional and compatible script to be used with both R >> versions I >> > previously stated? >> >> Hi, Jos?. >> >> The versions of DEseq are matched to the versions of bioconductor >> which are matched to the versions of R. In other words, the only way >> to match the versions of DEseq between two machines is to use the same >> version of R on both. Installing R in your home directory is not >> difficult, so I'd suggest you try that on your linux cluster since >> R-2.13 is pretty outdated at this point. >> >> Also, you'll want to ALWAYS use biocLite() to install packages, as >> detailed on the bioconductor website. This can avoid headaches with >> version mismatches in the future. >> >> Sean >> >> >> > Thanks in advance for your kind support. >> > >> > With best wishes >> > >> > JL >> > >> > -- >> > -- >> > Dr. Jos? Luis Lav?n Trueba >> > >> > Dpto. de Producci?n Agraria >> > Grupo de Gen?tica y Microbiolog?a >> > Universidad P?blica de Navarra >> > 31006 Pamplona >> > Navarra >> > SPAIN >> > >> > [[alternative HTML version deleted]] >> > >> > >> > _______________________________________________ >> > 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 >> > > > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 REPLYlink written 6.0 years ago by Sean Davis21k
Howdy, On Thu, Oct 4, 2012 at 9:41 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Oct 4, 2012 at 9:30 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: >> Hello Sean, >> >> The main problem with updating the R version of the servers is that I'm not >> the SysAdmin, and he told me that they couldn't update it at the moment >> because they have some processes and pipelines that need the old R version >> (2.13), so he can't update it (weird, isn't it?). That's why I was looking >> for such strange compatibility... >> Anyway, due to my current low level on R scripting, when I come across a >> command that isn't functional I don't really know what to do but trying to >> use another manual version hoping the code there will fix it...but I've had >> no luck with that at the moment. That's why I asked about this. >> I'll keep trying to make DEseq work, but I begin to feel stupid, reading >> everybody seems to be able to run it except myself. > > If you have a good relationship with your sysadmin, ask him/her to > help you to install R in your home directory. This is not hard to do > (hopefully, for a sysadmin) and will allow you to run a different > version of R than that already installed on the system. Really, doing > this will be much better than copying code from various versions of > packages to "just make it work". In fact, I bet you can do it w/o a sysadmin. Let's assume your username is jose (1) Log into your compute server (2) cd ~ ## you're likely already there Create directories to put the source code in as well as the compiled R (3) mkdir tmp (4) mkdir -p R/R-2.15 ## R will be installed here Let's get the source code and put it into tmp (5) cd tmp Get the code with curl or wget (whichever your system has) (6a) curl -O http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz ## or ## (6b) wget http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz Open it up, configure, compile, install (7) tar xvfz R-2.15.1.tar.gz (8) cd R-2.15.1 ## This is where you tell it where to install the new version of R ## Since it is in your home directory, your sysadmin doesn't need to be there ## and it won't affect anybody else's stuff (9) ./configure --prefix=/home/jose/R/R-2.15 (10) make && make install ... now you wait a while until it's all done ... Start R: (11) ~/R/R-2.15/bin/R biocLite() your packages and have fun. You may want to add /home/R/R-2.15/bin to your PATH -- you can ask your sysadmin how to do that, if you like ;-) -seve -- 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 REPLYlink written 6.0 years ago by Steve Lianoglou12k
Thank you everybody for your advice and opinions. I just wanted to be able to analyze my DE data and since I couldn't change R versions due to issues beyond my grasp... So, since I've the current R version in windows, I'll try to follow the newest manual commands there. ¿May any of you tell me which is the last version of DEseq manual? I'll keep up trying to make DEseq work, since I believe it's the tool of choice for my work unless any of you may tell me about a different one that could be easier to use without losing DEseq superb analysis capabilities. Thank you again for your time and attention. With best wishes JL 2012/10/4 Sean Davis <sdavis2@mail.nih.gov> > On Thu, Oct 4, 2012 at 9:30 AM, José Luis Lavín <jluis.lavin@unavarra.es> > wrote: > > Hello Sean, > > > > The main problem with updating the R version of the servers is that I'm > not > > the SysAdmin, and he told me that they couldn't update it at the moment > > because they have some processes and pipelines that need the old R > version > > (2.13), so he can't update it (weird, isn't it?). That's why I was > looking > > for such strange compatibility... > > Anyway, due to my current low level on R scripting, when I come across a > > command that isn't functional I don't really know what to do but trying > to > > use another manual version hoping the code there will fix it...but I've > had > > no luck with that at the moment. That's why I asked about this. > > I'll keep trying to make DEseq work, but I begin to feel stupid, reading > > everybody seems to be able to run it except myself. > > If you have a good relationship with your sysadmin, ask him/her to > help you to install R in your home directory. This is not hard to do > (hopefully, for a sysadmin) and will allow you to run a different > version of R than that already installed on the system. Really, doing > this will be much better than copying code from various versions of > packages to "just make it work". > > Sean > > > > Thank you for your swift answer, anyway > > > > Best wishes > > > > JL > > > > 2012/10/4 Sean Davis <sdavis2@mail.nih.gov> > > > >> On Thu, Oct 4, 2012 at 8:24 AM, José Luis Lavín < > jluis.lavin@unavarra.es> > >> wrote: > >> > Dear all, > >> > > >> > First of all I'd like to apologize for bothering you with such a naive > >> > question, but I've been told that this is the place to ask about this > >> > particular issue. > >> > > >> > I'm trying to perform a Differential Expresion analysis on some > RNA-seq > >> > experiments using DEseq package. I'm not very fluent with R yet, and > I'm > >> > facing some problems while using DEseq for the analysis. In my > >> institution > >> > the R version of the Linux servers system is 2.13.0 and the version I > >> > installed in my windows terminal is 2.15.2. > >> > I've retrieved multiple DEseq manual versions from the internet (dated > >> > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from > >> one > >> > to another and some are not supported in one or the other R versions I > >> have > >> > available. I need the R script to work in both versions and I don't > >> really > >> > know how to achieve it... > >> > Could you please help me solving this giving me some kind of advice on > >> how > >> > to get a functional and compatible script to be used with both R > >> versions I > >> > previously stated? > >> > >> Hi, José. > >> > >> The versions of DEseq are matched to the versions of bioconductor > >> which are matched to the versions of R. In other words, the only way > >> to match the versions of DEseq between two machines is to use the same > >> version of R on both. Installing R in your home directory is not > >> difficult, so I'd suggest you try that on your linux cluster since > >> R-2.13 is pretty outdated at this point. > >> > >> Also, you'll want to ALWAYS use biocLite() to install packages, as > >> detailed on the bioconductor website. This can avoid headaches with > >> version mismatches in the future. > >> > >> Sean > >> > >> > >> > Thanks in advance for your kind support. > >> > > >> > With best wishes > >> > > >> > JL > >> > > >> > -- > >> > -- > >> > Dr. José Luis Lavín Trueba > >> > > >> > Dpto. de Producción Agraria > >> > Grupo de Genética y Microbiología > >> > Universidad Pública de Navarra > >> > 31006 Pamplona > >> > Navarra > >> > SPAIN > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@r-project.org > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > -- > > -- > > Dr. José Luis Lavín Trueba > > > > Dpto. de Producción Agraria > > Grupo de Genética y Microbiología > > Universidad Pública de Navarra > > 31006 Pamplona > > Navarra > > SPAIN > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- -- Dr. José Luis Lavín Trueba Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by José Luis Lavín270
Hi, On Thu, Oct 4, 2012 at 10:42 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: > Thank you everybody for your advice and opinions. I just wanted to be able > to analyze my DE data and since I couldn't change R versions due to issues > beyond my grasp... > So, since I've the current R version in windows, I'll try to follow the > newest manual commands there. > ?May any of you tell me which is the last version of DEseq manual? It's always: http://bioconductor.org/packages/release/bioc/html/DESeq.html *currently* that is the same as: http://bioconductor.org/packages/2.11/bioc/html/DESeq.html Because 2.11 is the current release. The one that goes under active development which will be released with the *next* (always next) version of R/bioconductor is: http://bioconductor.org/packages/devel/bioc/html/DESeq.html 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 REPLYlink written 6.0 years ago by Steve Lianoglou12k
Hej Jos?! Start R, load the DESeq library and type in: vignette("DESeq") that will get you the PDF version of the manual corresponding to your installed version. Cheers, --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Oct 4, 2012, at 4:42 PM, Jos? Luis Lav?n wrote: > Thank you everybody for your advice and opinions. I just wanted to be able > to analyze my DE data and since I couldn't change R versions due to issues > beyond my grasp... > So, since I've the current R version in windows, I'll try to follow the > newest manual commands there. > ?May any of you tell me which is the last version of DEseq manual? > I'll keep up trying to make DEseq work, since I believe it's the tool of > choice for my work unless any of you may tell me about a different one that > could be easier to use without losing DEseq superb analysis capabilities. > > Thank you again for your time and attention. > > With best wishes > > JL > > 2012/10/4 Sean Davis <sdavis2 at="" mail.nih.gov=""> > >> On Thu, Oct 4, 2012 at 9:30 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> >> wrote: >>> Hello Sean, >>> >>> The main problem with updating the R version of the servers is that I'm >> not >>> the SysAdmin, and he told me that they couldn't update it at the moment >>> because they have some processes and pipelines that need the old R >> version >>> (2.13), so he can't update it (weird, isn't it?). That's why I was >> looking >>> for such strange compatibility... >>> Anyway, due to my current low level on R scripting, when I come across a >>> command that isn't functional I don't really know what to do but trying >> to >>> use another manual version hoping the code there will fix it...but I've >> had >>> no luck with that at the moment. That's why I asked about this. >>> I'll keep trying to make DEseq work, but I begin to feel stupid, reading >>> everybody seems to be able to run it except myself. >> >> If you have a good relationship with your sysadmin, ask him/her to >> help you to install R in your home directory. This is not hard to do >> (hopefully, for a sysadmin) and will allow you to run a different >> version of R than that already installed on the system. Really, doing >> this will be much better than copying code from various versions of >> packages to "just make it work". >> >> Sean >> >> >>> Thank you for your swift answer, anyway >>> >>> Best wishes >>> >>> JL >>> >>> 2012/10/4 Sean Davis <sdavis2 at="" mail.nih.gov=""> >>> >>>> On Thu, Oct 4, 2012 at 8:24 AM, Jos? Luis Lav?n < >> jluis.lavin at unavarra.es> >>>> wrote: >>>>> Dear all, >>>>> >>>>> First of all I'd like to apologize for bothering you with such a naive >>>>> question, but I've been told that this is the place to ask about this >>>>> particular issue. >>>>> >>>>> I'm trying to perform a Differential Expresion analysis on some >> RNA-seq >>>>> experiments using DEseq package. I'm not very fluent with R yet, and >> I'm >>>>> facing some problems while using DEseq for the analysis. In my >>>> institution >>>>> the R version of the Linux servers system is 2.13.0 and the version I >>>>> installed in my windows terminal is 2.15.2. >>>>> I've retrieved multiple DEseq manual versions from the internet (dated >>>>> 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from >>>> one >>>>> to another and some are not supported in one or the other R versions I >>>> have >>>>> available. I need the R script to work in both versions and I don't >>>> really >>>>> know how to achieve it... >>>>> Could you please help me solving this giving me some kind of advice on >>>> how >>>>> to get a functional and compatible script to be used with both R >>>> versions I >>>>> previously stated? >>>> >>>> Hi, Jos?. >>>> >>>> The versions of DEseq are matched to the versions of bioconductor >>>> which are matched to the versions of R. In other words, the only way >>>> to match the versions of DEseq between two machines is to use the same >>>> version of R on both. Installing R in your home directory is not >>>> difficult, so I'd suggest you try that on your linux cluster since >>>> R-2.13 is pretty outdated at this point. >>>> >>>> Also, you'll want to ALWAYS use biocLite() to install packages, as >>>> detailed on the bioconductor website. This can avoid headaches with >>>> version mismatches in the future. >>>> >>>> Sean >>>> >>>> >>>>> Thanks in advance for your kind support. >>>>> >>>>> With best wishes >>>>> >>>>> JL >>>>> >>>>> -- >>>>> -- >>>>> Dr. Jos? Luis Lav?n Trueba >>>>> >>>>> Dpto. de Producci?n Agraria >>>>> Grupo de Gen?tica y Microbiolog?a >>>>> Universidad P?blica de Navarra >>>>> 31006 Pamplona >>>>> Navarra >>>>> SPAIN >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>> >>> >>> >>> -- >>> -- >>> Dr. Jos? Luis Lav?n Trueba >>> >>> Dpto. de Producci?n Agraria >>> Grupo de Gen?tica y Microbiolog?a >>> Universidad P?blica de Navarra >>> 31006 Pamplona >>> Navarra >>> SPAIN >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> 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 >> > > > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 REPLYlink written 6.0 years ago by delhomme@embl.de1.2k
Hi Jose On 2012-10-04 15:30, Jos? Luis Lav?n wrote: > The main problem with updating the R version of the servers is that I'm not > the SysAdmin, and he told me that they couldn't update it at the moment > because they have some processes and pipelines that need the old R version > (2.13), so he can't update it (weird, isn't it?). That's why I was looking > for such strange compatibility... > Anyway, due to my current low level on R scripting, when I come across a > command that isn't functional I don't really know what to do but trying to > use another manual version hoping the code there will fix it...but I've had > no luck with that at the moment. That's why I asked about this. > I'll keep trying to make DEseq work, but I begin to feel stupid, reading > everybody seems to be able to run it except myself. A rather fundamental issue is that bioinformatics is a rapidly developing subject, and you have to stay current. Working with software version older than a few months is usually asking for trouble, especially when you are using cutting-edge techniques such as high-throughput sequencing. So: In the long run, there is simply no way getting your work done if you don't get a system with _current_ software. Either find a more helpful system administrator (yours is either lazy or incompetent: there is no problem in having two versions of R installed on the same machine), or learn to do that yourself. And never assume that there is any point in using a software manual vor version X of some software if what you have installed is version Y. Why should this ever work? Simon
ADD REPLYlink written 6.0 years ago by Simon Anders3.5k
0
6.0 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
See Sean's answer for more details, but I just wanted to note that you are trying to get a script to work across more then 1 year of development of the package. I would not expect that to work, given that a lot is happening with the sequencing packages these days. Kasper On Thu, Oct 4, 2012 at 8:24 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: > Dear all, > > First of all I'd like to apologize for bothering you with such a naive > question, but I've been told that this is the place to ask about this > particular issue. > > I'm trying to perform a Differential Expresion analysis on some RNA- seq > experiments using DEseq package. I'm not very fluent with R yet, and I'm > facing some problems while using DEseq for the analysis. In my institution > the R version of the Linux servers system is 2.13.0 and the version I > installed in my windows terminal is 2.15.2. > I've retrieved multiple DEseq manual versions from the internet (dated > 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one > to another and some are not supported in one or the other R versions I have > available. I need the R script to work in both versions and I don't really > know how to achieve it... > Could you please help me solving this giving me some kind of advice on how > to get a functional and compatible script to be used with both R versions I > previously stated? > > Thanks in advance for your kind support. > > With best wishes > > JL > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 COMMENTlink written 6.0 years ago by Kasper Daniel Hansen6.4k
0
6.0 years ago by
Spain
José Luis Lavín10 wrote:
Dear all, First of all I'd like to apologize for bothering you with such a naive question, but I've been told that this is the place to ask about this particular issue. I'm trying to perform a Differential Expresion analysis on some RNA- seq experiments using DEseq package. I'm not very fluent with R yet, and I'm facing some problems while using DEseq for the analysis. In my institution the R version of the Linux servers system is 2.13.0 and the version I installed in my windows terminal is 2.15.2. I've retrieved multiple DEseq manual versions from the internet (dated 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one to another and some are not supported in one or the other R versions I have available. I need the R script to work in both versions and I don't really know how to achieve it... Could you please help me solving this giving me some kind of advice on how to get a functional and compatible script to be used with both R versions I previously stated? Thanks in advance for your kind support. With best wishes JL This e-mail comes from CIC bioGUNE. The e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised dissemination or copying of this e-mail or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this e-mail in error, please notify or telephone + 34 944 06 13 00 and delete it from your system. Please consider the environment before printing this email [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by José Luis Lavín10
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