[BioC] Creating an new exprSet

[Rafael A. Irizarry]

the latest version of Biobase has a read.exprSet function you can use to
read in data.



On Wed, 29 Oct 2003, Marcelo Luiz de Laia wrote:

> Hi people,
> 
> I read the Vignette of VSN and the html help for VSN and exprSet.
> 
> I don't understand how do I do to create one new exprSet from my datas.
> 
> Could Someone send me an exprSet model?
> How many files should I have?
> I have a 3 file (var_suscep_rep1.txt, var_suscep_rep2.txt,
> var_suscep_rep3.txt) with the following format:
> 
> Gene_ID Ctrl_Bkgd Ctrl_sVol Ctrl_Vol Data_Bkgd Data_sVol Data_Vol
>  gene1    30.2       1.9      32.2      7.4       1.1       8.4
> 
> Ctrl = Untreated
> Data = Treated
> Bkgd = background
> Vol = Intensity of foreground (spot)
> sVol = Vol - Bkgd
> 
> Can I make a file with Ctrl_sVol and Data_sVol for each replicate or one
> file for Crtl_sVol and another file for Data_sVol?
> 
> new('exprSet',
> exprs = ...., # What should I put here considering the data above?
> se.exprs = ...., # What should I put here considering the data above?
> phenoData = ...., # This a file? What should I put here considering the data
> above?
> annotation = ...., # What should I put here considering the data above?
> description = ...., # What should I put here considering the data above?
> notes = ...., # What should I put here considering the data above?
> )
> 
> How do I do to load my datas into exprSet?
> 
> Thanks
> 
> Marcelo Luiz de Laia, M.Sc.
> Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular
> Universidade Estadual Paulista - UNESP
> Via de Acesso Prof. Paulo Donato Castelane, Km 05
> 14.884-900 - Jaboticabal, SP, Brazil
> PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
> Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com
> ---
> 
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