[BioC] [how to] cel files -> directly to expression level

[Kasper Daniel Hansen]

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 at biostat.ku.dk>
> To: "s_r" <s_r at poczta.fm>
> Cc: <Bioconductor at 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 at 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