R scripts from AffylmGUI
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Marcos Pinho ▴ 200
@marcos-pinho-3584
Last seen 7.7 years ago
Hi list, I am new to the list and trying to learn how to use the bioconductor suite to analyse affymetrix microarray data! Could anybody tell me how to get the R scripts from my analysis while using the affylmGUI ? regards, Dr. Marcos B. Pinho Programa de Engenharia Química - PEQ Laboratório de Engenharia de Cultivos Celulares- LECC Universidade Federal do Rio de Janeiro - UFRJ Instituto Nacional de Câncer - INCA Rio de Janeiro - Brasil [[alternative HTML version deleted]]
Microarray affylmGUI Microarray affylmGUI • 684 views
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@keith-satterley-1452
Last seen 7.5 years ago
Australia
Hi Marcos, not sure what you mean by getting the R scripts. By typing sessionInfo() in the R window after loading affylmGUI you can see that it also uses packages affyio, affy, Biobase and limma, among others. You can view the R code of any function by for example: search() - this gives the position of packages in the search path. ls(pos=7) - this will list functions from the seventh package in the searchpath ,limma in this case. To see the R code for a function, type the name of the function (without brackets). For example: lmFit - this will show you the R code for the lmFit function. The functions in the affylmGUI package are mainly to do with providing a Graphical User Interface to use functions from the other packages. Examining code this way can get very complicated and beyond a beginner. You may benefit more from reading the limma users guide: library(limma) limmaUsersGuide() or ?limma This shows the help package for limma functions. Similarly for other packages. cheers, Keith ======================== Keith Satterley affylmGUI maintainer. Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia ======================= Marcos Pinho wrote: > Hi list, > I am new to the list and trying to learn how to use the bioconductor suite > to analyse affymetrix microarray data! Could anybody tell me how to get the > R scripts from my analysis while using the affylmGUI ? > > regards, > > Dr. Marcos B. Pinho > Programa de Engenharia Qu?mica - PEQ > Laborat?rio de Engenharia de Cultivos Celulares- LECC > Universidade Federal do Rio de Janeiro - UFRJ > Instituto Nacional de C?ncer - INCA > Rio de Janeiro - Brasil > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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
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Hi Marcos, After a prompt by Vincent Carey off list to make a log file, (thanks Vincent), you maybe interested in using the "Export Html Report" function under the File Menu. It is not a log of commands given, but a report of the normalization method used, design and contrast matrices and the outputs created by you using affylmGUI, together with the date and versions of R software used for the analysis. Hope this helps, Keith ======================== Keith Satterley Keith Satterley wrote: > Hi Marcos, > > not sure what you mean by getting the R scripts. By typing sessionInfo() > in the R window after loading affylmGUI you can see that it also uses > packages affyio, affy, Biobase and limma, among others. > > You can view the R code of any function by for example: > search() - this gives the position of packages in the search path. > ls(pos=7) - this will list functions from the seventh package in the > searchpath ,limma in this case. > To see the R code for a function, type the name of the function (without > brackets). For example: > lmFit - this will show you the R code for the lmFit function. > > The functions in the affylmGUI package are mainly to do with providing a > Graphical User Interface to use functions from the other packages. > > Examining code this way can get very complicated and beyond a beginner. > You may benefit more from reading the limma users guide: > > library(limma) > limmaUsersGuide() > > or > > ?limma > > This shows the help package for limma functions. Similarly for other > packages. > > cheers, > > Keith > > ======================== > Keith Satterley > affylmGUI maintainer. > Bioinformatics Division > The Walter and Eliza Hall Institute of Medical Research > Parkville, Melbourne, > Victoria, Australia > ======================= > > Marcos Pinho wrote: >> Hi list, >> I am new to the list and trying to learn how to use the bioconductor >> suite >> to analyse affymetrix microarray data! Could anybody tell me how to >> get the >> R scripts from my analysis while using the affylmGUI ? >> >> regards, >> >> Dr. Marcos B. Pinho >> Programa de Engenharia Qu?mica - PEQ >> Laborat?rio de Engenharia de Cultivos Celulares- LECC >> Universidade Federal do Rio de Janeiro - UFRJ >> Instituto Nacional de C?ncer - INCA >> Rio de Janeiro - Brasil >> >> [[alternative HTML version deleted]] >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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
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