[BioC] Creating an new exprSet

[Marcelo Luiz de Laia]

Dear All,

I make an exprSet using the read.exprSet function (see below).

My file have 3575 genes, but I have 7 colunms (3 untreated replicates and 3
treated replicates). The first is the Gene_ID colunm.

My procedure is correct?

My doubt happened when I executed an eSet and I observed that it returned 7
samples. Does it consider the column gene_id as being a sample?

> KarinaSusc<-read.table("Suscetivel_R.txt",header=TRUE,sep="\t",as.is=TRUE)
> write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t", row.names
=TRUE, col.names = TRUE)
> eSet <- read.exprSet(testFile)
> eSet
Expression Set (exprSet) with
        3575 genes
        7 samples
                 phenoData object with 1 variables and 7 cases
         varLabels
                sample: arbitrary numbering

Thanks a lot

Marcelo

> -----Original Message-----
> From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu]
> Sent: quinta-feira, 30 de outubro de 2003 00:52
> To: Marcelo Luiz de Laia
> Cc: Ethz. Ch
> Subject: Re: [BioC] Creating an new exprSet
>
>
> 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
> > ---
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
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