Hi, On Wed, Jan 6, 2010 at 4:35 PM, cihan inan <cihan253 at="" gmail.com=""> wrote: > Well I am a biology student at university. and next year I will be a master > student. I am planning to be in bioinformatics department. that's why I need > to learn as much as I can. But at first I want to learn analysis about > microarrays. from beginning to the end. ?normalisation etc... I have 6 > months and I think it is enough to learn a lot of think about microarrays. No simple answer, but try this after installing Bioconductor. R> library(affy) R> openVignette() Select the 1st one (eg. the primer). It deals with getting your feet wet w/ affy arrays (some normalization/quality control stuff, too). Check out the papers in the References section too for more info. As you get going, you'll quickly find the need to use limma as well: a package to call differentially expressed genes between samples. It's a very flexible, which is great, but also a bit complex since it's so flexible. Load the library and fire up its user's guide R> library(limma) R> limmaUsersGuide() Lots of good references in its Bibliography. 6 months is *just about* enough time to get through that user guide plus refs (and their refs) + getting comfortable w/ R and Bioconductor ... you might find you'd like even more time, though ... let us now :-) Good luck, -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

Don't know what you meant by "application", but application of Bioconductor to the analysis of micrarray data seems quite popular. Why don't you try to get hold of any recent paper that uses microarray data, go to where the authors deposited their data - ArrayExpress, GEO etc., try to download their raw data and then repeat their transformation/normalization (hopefully you can find a case when raw data was deposited) and identify differentially expressed genes? Authors would usually list Bioconductor libraries in methods section. And if after that you still have some time left within your 6 months - similar thing can be done with a paper to do with new generation sequencing data. Aslo, I think your english is even funnier than mine. I found that going to pubs with people who speak english to be fairly helpful :) Sergei 2010/1/6 cihan inan <cihan253@gmail.com> > Well I am a biology student at university. and next year I will be a master > student. I am planning to be in bioinformatics department. that's why I > need > to learn as much as I can. But at first I want to learn analysis about > microarrays. from beginning to the end. normalisation etc... I have 6 > months and I think it is enough to learn a lot of think about microarrays. > > 2010/1/6 James W. MacDonald <jmacdon@med.umich.edu> > > > cihan inan wrote: > > > >> Hi all, > >> > >> I am new with bioconductor and I want to learn all apps. but I want to > >> have > >> a to do list. What's you opinion? What should I do? and which > application > >> must be the first to start? > >> > > > > I seriously doubt you want to learn how to use all 353 packages. Perhaps > > you could tell us what sort of data you have and what you are planning to > do > > with it? > > > > Best, > > > > Jim > > > > > > > >> > >> > >> ----------------------------------------------------------------- ------- > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@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 > > Douglas Lab > > University of Michigan > > Department of Human Genetics > > 5912 Buhl > > 1241 E. Catherine St. > > Ann Arbor MI 48109-5618 > > 734-615-7826 > > ********************************************************** > > Electronic Mail is not secure, may not be read every day, and should not > be > > used for urgent or sensitive issues > > > > > > -- > Özgürlük için...http://www.pardus.org.tr/ > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- EMBL-EBI and Wellcome Trust Sanger Institute tel: 00441223492675 [[alternative HTML version deleted]]

Hi, I do not know if you already saw this: http://www.bioconductor.org/GettingStarted Extensive information carefully categorized. Saroj cihan inan wrote: > Well I am a biology student at university. and next year I will be a master > student. I am planning to be in bioinformatics department. that's why I need > to learn as much as I can. But at first I want to learn analysis about > microarrays. from beginning to the end. normalisation etc... I have 6 > months and I think it is enough to learn a lot of think about microarrays. > > 2010/1/6 James W. MacDonald <jmacdon at="" med.umich.edu=""> > > >> cihan inan wrote: >> >> >>> Hi all, >>> >>> I am new with bioconductor and I want to learn all apps. but I want to >>> have >>> a to do list. What's you opinion? What should I do? and which application >>> must be the first to start? >>> >>> >> I seriously doubt you want to learn how to use all 353 packages. Perhaps >> you could tell us what sort of data you have and what you are planning to do >> with it? >> >> Best, >> >> Jim >> >> >> >> >>> ------------------------------------------------------------------ ------ >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> 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

Hi, Because BioConductor is so large, it can be hard for new investigators (or older investigators who haven't used it regularly) to figure out where to start . To help address this issue, we have developed an experimental tool that provides an interactive graphical overview of BioConductor. The tool is available at http://bioinformatics.mdanderson.org/BioCycle Just follow the link from that page to the "Interactive Flash circular graph". The nodes in this graph represent different BioConductor packages, and the edges represent the "Depends" relationships. Each node links to the full package documentation at bioconductor.org. Under the same principle that we use for biological networks and pathways, it seems reasonable to assume that "hub nodes" are particularly important packages and might prove a good place to start. For instance, Biobase is the largest hub, with affy and limma fairly prominent secondary hubs. Reading about how the latter two packages work is probably a good place to start learning about how to apply BioConductor to microarrays. Best, Kevin cihan inan wrote: > Well I am a biology student at university. and next year I will be a master > student. I am planning to be in bioinformatics department. that's why I need > to learn as much as I can. But at first I want to learn analysis about > microarrays. from beginning to the end. normalisation etc... I have 6 > months and I think it is enough to learn a lot of think about microarrays. > > 2010/1/6 James W. MacDonald <jmacdon at="" med.umich.edu=""> > > >> cihan inan wrote: >> >> >>> Hi all, >>> >>> I am new with bioconductor and I want to learn all apps. but I want to >>> have >>> a to do list. What's you opinion? What should I do? and which application >>> must be the first to start? >>> >>> >> I seriously doubt you want to learn how to use all 353 packages. Perhaps >> you could tell us what sort of data you have and what you are planning to do >> with it? >> >> Best, >> >> Jim >> >> >> >> >>> ------------------------------------------------------------------ ------ >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> 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