[BioC] Creating an new exprSet
Marcelo Luiz de Laia
mlaia at fcav.unesp.br
Thu Oct 30 14:35:13 MET 2003
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?
> write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t", row.names
=TRUE, col.names = TRUE)
> eSet <- read.exprSet(testFile)
Expression Set (exprSet) with
phenoData object with 1 variables and 7 cases
sample: arbitrary numbering
Thanks a lot
> -----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
> Incoming mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.532 / Virus Database: 326 - Release Date: 27/10/2003
More information about the Bioconductor