Hi. I know R language a little so I've got a question to You. I'm asking You for help because i can't find it anywhere. I want to know how to get an expression level of genes from the .CEL file. I've found some information to do it with using a functions like rma or mas to get an object exprs from object of class affybatch. But I need raw expression level before apply any normalization algorithm (expression directly from cel files). Than I want to save it (expression level) with function write.exprs. Thank You very much, and sorry for my English... Sebastian [[alternative HTML version deleted]]

read.affybatch reads the file into an AffyBatch object. This object is very similar to an exprSet, and there is no normalization or anything going on. Afterwards you can use exprs() to acces the raw expression intensities. Kasper On Fri, May 06, 2005 at 08:34:27AM +0200, s_r wrote: > Hi. > > I know R language a little so I've got a question to You. I'm asking You for help because i can't find it anywhere. > > I want to know how to get an expression level of genes from the .CEL file. > I've found some information to do it with using a functions like rma or mas to get an object exprs from object of class affybatch. But I need raw expression level before apply any normalization algorithm (expression directly from cel files). Than I want to save it (expression level) with function write.exprs. > > > Thank You very much, and sorry for my English... > Sebastian > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen

It seems that you want to summarize the probe intensities into a single numbr for each gene. This is not what I would consider "raw" data. Furthermore there is no transformation which is inheirently more "raw" than others. I think you need to read up a bit on summarizing methods. In case you want to do something else, please provide an example of how you want the output to look. Kasper On Fri, May 06, 2005 at 04:03:46PM +0200, s_r wrote: > But when I want to save the values into for example .txt file with function > write.exprs(x,file="a.txt") there is in the file 'a.txt' for example 500000 > positions in the one column. I want to have in first column a gene name and > in the next column expression of this gene (and there is for example 22000 > gens i that cel files). The number i've written 500000 is number of probes > in raw cel file it isn't a gene expression, but pm and mm values if I had > understad it well. When I use functions like rma and mas on the object of > class affybatch, and when I save it with write.exprs I've got exactly what > I want (the columns with result). But with using for example RMA my cel is > converting and it isn't raw data any more. > > > > ----- Original Message ----- > From: "Kasper Daniel Hansen" <k.hansen@biostat.ku.dk> > To: "s_r" <s_r@poczta.fm> > Cc: <bioconductor@stat.math.ethz.ch> > Sent: Friday, May 06, 2005 8:38 AM > Subject: Re: [BioC] [how to] cel files -> directly to expression level > > > >read.affybatch reads the file into an AffyBatch object. This object is > >very similar to an exprSet, and there is no normalization or anything > >going on. Afterwards you can use exprs() to acces the raw expression > > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor@stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >-- > >Kasper Daniel Hansen, Research Assistant > >Department of Biostatistics, University of Copenhagen > > > > > > > ---------------------------------------------------------------------- > NAJTANSZY KREDYT mieszkaniowy w Polsce! 100 tys. zl juz od 333 zl > miesiecznie! Kliknij! > >>>http://clk.tradedoubler.com/click?p=20565&a=1029167&g=1130041 > > -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen