[BioC] expression values

[Ben Bolstad]

JustRMA should require bgversion=2 also. If you go outside the defaults
it is still possible to get different results.

in general

eset1 <-
expresso(data,bgcorrect.method="rma",normalize.method="quantiles",
pmcorrect.method="pmonly",summary.method="medianpolish")

eset2 <- rma(data)

and 

eset3 <- justRMA(filenames)


should give you identical sets of expression values.

How many chips are you trying to do? What operating system are you
using? How much memory do you have? 


Ben



On Sun, 2003-06-08 at 13:05, Jingqin luo wrote:
> Thank you for your response. But after I installed the
> new version of R and bioconductor , the expression
> values obtained from the three functions(expresso,rma
> and justRMA) are still different. Am I wrong in
> setting some of the auguments?
> Here are the functions I used:
> (1)affy3chip1 <- ReadAffy ( filenames = c ( "
> 1674.cel" ,"1675.cel"))
> 
> try.rma<-expresso(affy3chip1,bgcorrect.method="rma",normalize.method="quantiles",pmcorrect.method="pmonly",summary.method="medianpolish")
> 
> (2)try.rma1 <- rma( affy3chip1, verbose=TRUE,
> destructive=TRUE,normalize=TRUE,background=TRUE,bgversion=2)
> (3)try.rma2 <- justRMA ( filenames =
> c("1674.cel","1675.cel"),normalize=TRUE,background=TRUE,bgversion=1,destructive=TRUE)
> 
> BTW,besides justRMA, is ther any other function used
> for calculation of expression values and at the same
> time avoid exhausting the memory?
> 
> 
> 
> --- Ben Bolstad <bolstad at stat.berkeley.edu> wrote:
> > This should be fixed in the 1.2 release. You should
> > be getting the same
> > values from each of three methods.
> > 
> > Ben
> > 
> > 
> > 
> > 
> > On Thu, 2003-06-05 at 09:50, Jingqin luo wrote:
> > > Hi,there, 
> > >   Recently, I used the 3 functions expresso, rma
> > and
> > > justRMA to compute the expression for a same chip.
> > The
> > > 3 outputs are not the same, kind of shifting above
> > a
> > > little bit. Shouldn't they be same or is there a
> > way
> > > to keep them the same?
> > > Thanks and have a good day!
> > > 
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > >
> >
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > -- 
> > Ben Bolstad <bolstad at stat.berkeley.edu>
> > 
> 
> 
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>