Hi.
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
>
> --
> 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.
You received this message because you are subscribed to the Google Groups
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