[BioC] R scripts from AffylmGUI

Keith Satterley keith at wehi.EDU.AU
Thu Jul 23 02:17:00 CEST 2009

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 packages.



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 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
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