correlation between two pathways' genes
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Alyaa Mahmoud ▴ 440
@alyaa-mahmoud-4670
Last seen 4.7 years ago
Dear Group I would like to find if the genes of two different pathways are correlated or anti-correlated or no correlation at all. The number of genes in the two pathways are different, that's why a simple scatter plot will not be effective. Is there a simple way I can do this ? Thank you very much Alyaa Mahmoud Jr Computational Biologist Biology Department American University in Cairo, Egypt alya.mahmoud@aucegypt.edu +2 0100 17 31 389 -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
Pathways Pathways • 1.1k views
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Paul Geeleher ★ 1.3k
@paul-geeleher-2679
Last seen 10.2 years ago
I think you'd first have to summarize the "expression level" of each pathway somehow, the easiest thing to do is probably to summarize them by their median. Then calculate the corrleation between the median of each of your pathways. Paul. On Sat, Dec 15, 2012 at 4:13 PM, Alyaa Mahmoud <alyamahmoud at="" gmail.com=""> wrote: > Dear Group > > I would like to find if the genes of two different pathways are correlated > or anti-correlated or no correlation at all. The number of genes in the two > pathways are different, that's why a simple scatter plot will not be > effective. Is there a simple way I can do this ? > > Thank you very much > Alyaa Mahmoud > > Jr Computational Biologist > Biology Department > American University in Cairo, Egypt > alya.mahmoud at aucegypt.edu > +2 0100 17 31 389 > > -- > Alyaa Mahmoud > > "Love all, trust a few, do wrong to none"- Shakespeare > > [[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. Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com
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Thanks a lot Paul for the suggestion. On Sun, Dec 16, 2012 at 2:50 PM, Paul Geeleher <paulgeeleher@gmail.com>wrote: > I think you'd first have to summarize the "expression level" of each > pathway somehow, the easiest thing to do is probably to summarize them > by their median. Then calculate the corrleation between the median of > each of your pathways. > > Paul. > > On Sat, Dec 15, 2012 at 4:13 PM, Alyaa Mahmoud <alyamahmoud@gmail.com> > wrote: > > Dear Group > > > > I would like to find if the genes of two different pathways are > correlated > > or anti-correlated or no correlation at all. The number of genes in the > two > > pathways are different, that's why a simple scatter plot will not be > > effective. Is there a simple way I can do this ? > > > > Thank you very much > > Alyaa Mahmoud > > > > Jr Computational Biologist > > Biology Department > > American University in Cairo, Egypt > > alya.mahmoud@aucegypt.edu > > +2 0100 17 31 389 > > > > -- > > Alyaa Mahmoud > > > > "Love all, trust a few, do wrong to none"- Shakespeare > > > > [[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. Paul Geeleher > School of Mathematics, Statistics and Applied Mathematics > National University of Ireland > Galway > Ireland > -- > www.bioinformaticstutorials.com > -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
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