[BioC] R scripts from AffylmGUI
keith at wehi.EDU.AU
Thu Jul 23 04:23:03 CEST 2009
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 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:
> This shows the help package for limma functions. Similarly for other
> 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
>> to analyse affymetrix microarray data! Could anybody tell me how to
>> get the
>> R scripts from my analysis while using the affylmGUI ?
>> 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]]
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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