[BioC] R scripts from AffylmGUI

[Keith Satterley]

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 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]]
> 
> 
> 
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