Thanks a lot for the explanation and reference.
Rahul
On Oct 10, 11:18 am, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi.
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> On Mon, Oct 10, 2011 at 9:01 AM, rahul <v.rahul.sim...@gmail.com> wrote:
> > Hello Henrik,
>
> > I am using the follwing commands to process my data.
>
> > library(aroma.affymetrix)
> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> > chipType <- "HuEx-1_0-st-v2"
> > cdf <- AffymetrixCdfFile$byChipType(chipType, tag="web,v_cdf")
> > print(cdf)
> > cs <- AffymetrixCelSet$byName("Sample", cdf=cdf)
> > print(cs)
> > setCdf(cs, cdf)
> > bc <- RmaBackgroundCorrection(cs, tag="web,v_cdf")
> > csBC <- process(bc,verbose=verbose)
> > qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> > print(qn)
> > csN <- process(qn, verbose=verbose)
> > plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
> > print(plmEx)
> > fit(plmEx, verbose=verbose)
> > cesEx <- getChipEffectSet(plmEx)
> > trFit <- extractDataFrame(cesEx, addNames=TRUE)
>
> > My question: the resulting data frame (trFit) has values in regular
> > scale(same scale as intensity values in .cel files). I expected them
> > to be in log2 scale. Did i miss a step or we get the values only in
> > the regular scale.
>
> Yes, this is correct. In the Aroma framework, all data/signals are
> (intentionally) stored on the original scale, with one of the reasons
> being that negative and zero signal estimates cannot be represented on
> the log scale. The original/intensity scale is simply the most
> generic one. Note that parameters may still have been estimated on
> say the log2 scale, but before being saved they are backtransformed to
> the original scale. It's been awhile, but there has been some more
> posts/discussion on this back in time.
>
> You need to log2() yourself, e.g. vignette 'Using the GenomeGraphs
> package with FIRMA' [http://aroma-project.org/node/61].
>
> /Henrik
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> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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