Correlation analysis
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Minh Bui ▴ 20
@minh-bui-4947
Last seen 6.9 years ago
Hi everyone, I am new to Bioconductor and R. I did search through the list for my problem but i can't find it. I am sorry if this question has been asked. I would like to perform a correlation analysis between a hiv data and gene expression. Basically, i have a file that contains: hiv_name, start_position, end_position, chromosome. I would like to see if these data has anything to do with the location of our genes (I also have another file contains gene_name, start_position, end_position, chromosome). What functions that allow me to do this? Hopefully someone can guide me to the right direction. Thank you very much, -- ---------------------------------------------------------------------- -------------- Minh Bui Bioinformatic Research, MicroBiome Analysis Center George Mason University, Prince William Campus 10900 University Boulevard, MSN 4D4 Manassas, Virginia 20110 http://mbac.gmu.edu ---------------------------------------------------------------------- -------------- [[alternative HTML version deleted]]
Microbiome HIV Microbiome HIV • 776 views
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@sean-davis-490
Last seen 10 days ago
United States
Hi, Minh. By "correlation analysis", you mean that you want to find the gene closest to each HIV site? If so, take a look at the GenomicRanges package. If you are more of a web server point-and-click person, take a look at using galaxy: http://main.g2.bx.psu.edu/ Sean On Mon, Nov 7, 2011 at 5:52 PM, Minh Bui <buiduyminh at="" gmail.com=""> wrote: > Hi everyone, > > I am new to Bioconductor and R. I did search through the list for my > problem but i can't find it. I am sorry if this question has been asked. > > I would like to perform a correlation analysis between a hiv data and gene > expression. > > Basically, i have a file that contains: hiv_name, start_position, > end_position, chromosome. I would like to see if these data has anything to > do with the location of our genes (I also have another file contains > gene_name, start_position, end_position, chromosome). > > What functions that allow me to do this? > > Hopefully someone can guide me to the right direction. > > > Thank you very much, > > -- > > -------------------------------------------------------------------- ---------------- > Minh Bui > Bioinformatic Research, MicroBiome Analysis Center > George Mason University, Prince William Campus > 10900 University Boulevard, MSN 4D4 > Manassas, Virginia ?20110 > http://mbac.gmu.edu > -------------------------------------------------------------------- ---------------- > > ? ? ? ?[[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 >
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HI Sean, Thank you for the quick answer. By correlation analysis, I mean I want to see if those HIV sequences fall into the genes or not. If so, what kind of test I should do? I will check those two sources out. Thanks, On Mon, Nov 7, 2011 at 5:56 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > Hi, Minh. > > By "correlation analysis", you mean that you want to find the gene > closest to each HIV site? If so, take a look at the GenomicRanges > package. > > If you are more of a web server point-and-click person, take a look at > using galaxy: > > http://main.g2.bx.psu.edu/ > > Sean > > > On Mon, Nov 7, 2011 at 5:52 PM, Minh Bui <buiduyminh@gmail.com> wrote: > > Hi everyone, > > > > I am new to Bioconductor and R. I did search through the list for my > > problem but i can't find it. I am sorry if this question has been asked. > > > > I would like to perform a correlation analysis between a hiv data and > gene > > expression. > > > > Basically, i have a file that contains: hiv_name, start_position, > > end_position, chromosome. I would like to see if these data has anything > to > > do with the location of our genes (I also have another file contains > > gene_name, start_position, end_position, chromosome). > > > > What functions that allow me to do this? > > > > Hopefully someone can guide me to the right direction. > > > > > > Thank you very much, > > > > -- > > > > > -------------------------------------------------------------------- ---------------- > > Minh Bui > > Bioinformatic Research, MicroBiome Analysis Center > > George Mason University, Prince William Campus > > 10900 University Boulevard, MSN 4D4 > > Manassas, Virginia 20110 > > http://mbac.gmu.edu > > > -------------------------------------------------------------------- ---------------- > > > > [[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 > > > -- ---------------------------------------------------------------------- -------------- Minh Bui Bioinformatic Research, MicroBiome Analysis Center George Mason University, Prince William Campus 10900 University Boulevard, MSN 4D4 Manassas, Virginia 20110 http://mbac.gmu.edu ---------------------------------------------------------------------- -------------- [[alternative HTML version deleted]]
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On Mon, Nov 7, 2011 at 6:00 PM, Minh Bui <buiduyminh at="" gmail.com=""> wrote: > HI Sean, > > Thank you for the quick answer. > > By correlation analysis, I mean I want to see if those HIV sequences fall > into the genes or not. If so, what kind of test I should do? Hi, Minh. Either source I sent should deal with that question easily. Overlaps of two sets of genomic regions are what both deal with very well. Sean > I will check those two sources out. > > Thanks, > > > > > On Mon, Nov 7, 2011 at 5:56 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> Hi, Minh. >> >> By "correlation analysis", you mean that you want to find the gene >> closest to each HIV site? ?If so, take a look at the GenomicRanges >> package. >> >> If you are more of a web server point-and-click person, take a look at >> using galaxy: >> >> http://main.g2.bx.psu.edu/ >> >> Sean >> >> >> On Mon, Nov 7, 2011 at 5:52 PM, Minh Bui <buiduyminh at="" gmail.com=""> wrote: >> > Hi everyone, >> > >> > I am new to Bioconductor and R. I did search through the list for my >> > problem but i can't find it. I am sorry if this question has been asked. >> > >> > I would like to perform a correlation analysis between a hiv data and >> gene >> > expression. >> > >> > Basically, i have a file that contains: hiv_name, start_position, >> > end_position, chromosome. I would like to see if these data has anything >> to >> > do with the location of our genes (I also have another file contains >> > gene_name, start_position, end_position, chromosome). >> > >> > What functions that allow me to do this? >> > >> > Hopefully someone can guide me to the right direction. >> > >> > >> > Thank you very much, >> > >> > -- >> > >> > >> ------------------------------------------------------------------- ----------------- >> > Minh Bui >> > Bioinformatic Research, MicroBiome Analysis Center >> > George Mason University, Prince William Campus >> > 10900 University Boulevard, MSN 4D4 >> > Manassas, Virginia ?20110 >> > http://mbac.gmu.edu >> > >> ------------------------------------------------------------------- ----------------- >> > >> > ? ? ? ?[[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 >> > >> > > > > -- > > -------------------------------------------------------------------- ---------------- > Minh Bui > Bioinformatic Research, MicroBiome Analysis Center > George Mason University, Prince William Campus > 10900 University Boulevard, MSN 4D4 > Manassas, Virginia ?20110 > http://mbac.gmu.edu > -------------------------------------------------------------------- ---------------- > > ? ? ? ?[[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 >
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