Microarray data analysis
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Hi Friends, I want to use Bioconductor for microarray data analysis for that I need one example data on which I can try R codes? Can you please suggest start point for learning Bioconductor. Which package I should start with? Thanks. -- output of sessionInfo(): no -- Sent via the guest posting facility at bioconductor.org.
Microarray Microarray • 1.7k views
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@steve-lianoglou-2771
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Hi, On Sat, Mar 22, 2014 at 8:12 AM, Prabhakar [guest] <guest at="" bioconductor.org=""> wrote: > > Hi Friends, > I want to use Bioconductor for microarray data analysis for that I need one example data on which I can try R codes? Can you please suggest start point for learning Bioconductor. Which package I should start with? Thanks. For microarray analysis, you'll need a very good reason to not go with limma. You're going to want to thoroughly ingest its user's guide: http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst /doc/usersguide.pdf For more general bioconductor overviews, click through the different years's worth of materials from different workshops listed here: http://www.bioconductor.org/help/course-materials/ For microarray specific analyses, I guess you will find a greater fraction of them in earlier years, just browse through the different stuff there ... there's a lot to learn. http://www.bioconductor.org/help/course-materials/ Lastly, this: https://www.edx.org/course/harvardx/harvardx-ph525x-data-analysis- genomics-1401 HTH, -steve -- Steve Lianoglou Computational Biologist Genentech
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@prabhakar-ghorpade-6464
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Hi Friends,    I want to use Bioconductor for microarray data analysis for that I need one example data on which I can try R codes? Can you please suggest start point for learning Bioconductor. Which package I should start with? Thanks. [[alternative HTML version deleted]]
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For microarray data analysis, I would starting with the limma package. The User Guide is a great resource, so I would suggest reading sections of it to get you going. Sean On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade < prabhakar_ghorpade@yahoo.co.in> wrote: > Hi Friends, > I want to use Bioconductor for microarray data analysis for that I need > one example data on which I can try R codes? Can you please suggest start > point for learning Bioconductor. Which package I should start with? Thanks. > [[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 > [[alternative HTML version deleted]]
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>From the http://www.bioconductor.org/help/ page, check out the "Oligonucleotide arrays" link which has example data and workflows. On Sat, Mar 22, 2014 at 11:22 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > For microarray data analysis, I would starting with the limma package. The > User Guide is a great resource, so I would suggest reading sections of it > to get you going. > > Sean > > > > On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade < > prabhakar_ghorpade@yahoo.co.in> wrote: > > > Hi Friends, > > I want to use Bioconductor for microarray data analysis for that I > need > > one example data on which I can try R codes? Can you please suggest start > > point for learning Bioconductor. Which package I should start with? > Thanks. > > [[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 > > > > [[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 > -- Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org [[alternative HTML version deleted]]
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Hello, Thanks for reply.  I am trying to run limma with user guide instructions but from page 11 of user guide. I am getting following error > targets <- readTargets("targets.txt") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") :   cannot open file 'targets.txt': No such file or directory  How can I proceed with it? Did I need target.txt file of my own or does limma has example file in its package? Dr. Ghorpade Prabhakar B. PhD Scholar ( Veterinary Biochemistry), IVRI, Izatnagar, Bareilly, U.P., India On Saturday, 22 March 2014 11:43 PM, Levi Waldron <levi.waldron@hunter.cuny.edu> wrote: >From the http://www.bioconductor.org/help/ page, check out the "Oligonucleotide arrays" link which has example data and workflows. On Sat, Mar 22, 2014 at 11:22 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: For microarray data analysis, I would starting with the limma package. The >User Guide is a great resource, so I would suggest reading sections of it >to get you going. > >Sean > > > > >On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade < >prabhakar_ghorpade@yahoo.co.in> wrote: > >> Hi Friends, >>    I want to use Bioconductor for microarray data analysis for that I need >> one example data on which I can try R codes? Can you please suggest start >> point for learning Bioconductor. Which package I should start with? Thanks. >>         [[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 > >> > >        [[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 > -- Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org [[alternative HTML version deleted]]
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Hi, On Sun, Mar 23, 2014 at 6:40 AM, prabhakar ghorpade <prabhakar_ghorpade at="" yahoo.co.in=""> wrote: > Hello, > > Thanks for reply. I am trying to run limma with user guide instructions but from page 11 of user guide. I am getting following error >> targets <- readTargets("targets.txt") > Error in file(file, "rt") : cannot open the connection > In addition: Warning message: > In file(file, "rt") : > cannot open file 'targets.txt': No such file or directory > > How can I proceed with it? Did I need target.txt file of my own or does limma has example file in its package? Treat the user's guide like something of a book. Read through it in its entirety first before you start running your analysis. Although it is briefly mentioned on page 11 what the targets file is, you'll see on page 14 what exactly goes into it. From there you will realize that the targets.txt file needs to be something that you have to provide. -steve -- Steve Lianoglou Computational Biologist Genentech
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On Sun, Mar 23, 2014 at 9:40 AM, prabhakar ghorpade < prabhakar_ghorpade@yahoo.co.in> wrote: > Hello, > > Thanks for reply. I am trying to run limma with user guide instructions > but from page 11 of user guide. I am getting following error > > targets <- readTargets("targets.txt") > Error in file(file, "rt") : cannot open the connection > In addition: Warning message: > In file(file, "rt") : > cannot open file 'targets.txt': No such file or directory > The limma usersguide.pdf manual is not created during package build, so the code in the manual isn't self-standing and you do have to create your own targets.txt. The LIMMA manual is so extensive that I assume this is because it would take too long to create during package building. [[alternative HTML version deleted]]
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Thanks for reply Sean,             Did I need to go through Bioconductor Case Studies. I am not sure if I should proceed with it or not as book is published in 2008. Could it be outdated in current context of microarray analysis. Sincerely, Prabhakar Dr. Ghorpade Prabhakar B. PhD Scholar ( Veterinary Biochemistry), IVRI, Izatnagar, Bareilly, U.P., India On Saturday, 22 March 2014 8:53 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: For microarray data analysis, I would starting with the limma package. The User Guide is a great resource, so I would suggest reading sections of it to get you going. Sean On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade <prabhakar_ghorpade@yahoo.co.in> wrote: Hi Friends, >   I want to use Bioconductor for microarray data analysis for that I need one example data on which I can try R codes? Can you please suggest start point for learning Bioconductor. Which package I should start with? Thanks. >        [[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 > [[alternative HTML version deleted]]
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Hi, Prabhaka. Unfortunately, like in most scientific disciplines, there is no simple "guide" that is going to give you all you need to know. The book is a great resource, though it is a bit dated. You'll have to make your own decisions about the value of such materials based on your goals and background. Sean On Sun, Mar 23, 2014 at 10:52 AM, prabhakar ghorpade < prabhakar_ghorpade@yahoo.co.in> wrote: > Thanks for reply Sean, > Did I need to go through Bioconductor Case Studies. I am not > sure if I should proceed with it or not as book is published in 2008. Could > it be outdated in current context of microarray analysis. > > Sincerely, > Prabhakar > > Dr. Ghorpade Prabhakar B. > PhD Scholar ( Veterinary Biochemistry), > IVRI, > Izatnagar, > Bareilly, U.P., > India > > > > On Saturday, 22 March 2014 8:53 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > > For microarray data analysis, I would starting with the limma package. > The User Guide is a great resource, so I would suggest reading sections of > it to get you going. > > Sean > > > > > On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade < > prabhakar_ghorpade@yahoo.co.in> wrote: > > Hi Friends, > > I want to use Bioconductor for microarray data analysis for that I > need one example data on which I can try R codes? Can you please suggest > start point for learning Bioconductor. Which package I should start with? > Thanks. > > [[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 > > > [[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 > [[alternative HTML version deleted]]
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@gordon-smyth
Last seen 20 minutes ago
WEHI, Melbourne, Australia
The limma User's Guide includes a series of fully worked case studies starting in Chapter 16, and raw data is provided for all or most of them. The earlier chapters describe how one would use code. Readers are expected to adapt this advice to their own data and situation. The code you give occurs on page 12, and immediately before it the text says: "This is a quick overview of what an analysis might look like. ... We assume that the images have been analyzed using GenePix to produce a .gpr file for each array and that a targets file targets.txt has been prepared with a column containing the names of the .gpr files." This tells you that it is a hypothetical example. Realistically, microarray data is quite complex, and you should expect to have to read further than the second page of the "quick start" before knowing enough to do an analysis for yourself. Best wishes Gordon > Date: Sun, 23 Mar 2014 21:40:41 +0800 (SGT) > From: prabhakar ghorpade <prabhakar_ghorpade at="" yahoo.co.in=""> > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] Microarray data analysis > > Hello,? > > Thanks for reply. ?I am trying to run limma with user guide instructions but from page 11 of user guide. I am getting following error >> targets <- readTargets("targets.txt") > Error in file(file, "rt") : cannot open the connection > In addition: Warning message: > In file(file, "rt") : > ? cannot open file 'targets.txt': No such file or directory > > > > ?How can I proceed with it? Did I need target.txt file of my own or does limma has example file in its package?? > ? > ? > Dr. Ghorpade Prabhakar B. > PhD Scholar ( Veterinary Biochemistry), > IVRI, > Izatnagar, > Bareilly, U.P., > India > > > > On Saturday, 22 March 2014 11:43 PM, Levi Waldron <levi.waldron at="" hunter.cuny.edu=""> wrote: > >> From the http://www.bioconductor.org/help/ page, check out the "Oligonucleotide arrays" link which has example data and workflows. > > > > > On Sat, Mar 22, 2014 at 11:22 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > For microarray data analysis, I would starting with the limma package. ?The >> User Guide is a great resource, so I would suggest reading sections of it >> to get you going. >> >> Sean >> >> >> >> >> On Sat, Mar 22, 2014 at 11:14 AM, prabhakar ghorpade < >> prabhakar_ghorpade at yahoo.co.in> wrote: >> >>> Hi Friends, >>> ? ?I want to use Bioconductor for microarray data analysis for that I need >>> one example data on which I can try R codes? Can you please suggest start >>> point for learning Bioconductor. Which package I should start with? Thanks. ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:5}}
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