Hi Henrik,
Much thanks!I have tried "extractMatrix" and it works!
Yet another question merges...I used RMAExpress to extract the
expression level matrix some time ago (background adjusted, quantile
normalized and summarized using PLM) . I thought the outcomes of these
two preprocessing softwares (namely RMAExpress and aroma.affymetrix)
ought to be the same, yet they are not ...
I asked my mentor about this question of "inconsistency", and showed
him the "aroma.affymetrix-Analysis of small to very large Affymetrix
data sets"(which is written by you in August, 2007 =D).
He saw the descripton on page 48 that "# The SNP information contains
information about SNP fragment lengths.
cdf <- getCdf(ces)
si <-getSnpInformation(cdf)
fl <- getFragmentLengths(si)" and doubted whether I am using the right
software since the dataset I am currently working with measures the
DNA expression level.
I was wondering whether the steps I described above is ok for chips
that measure the DNA expression level, and if it ok, why the result is
inconsistent with the RMAExpress's result.
Thank you,
Anqi
On Jul 22, 5:09 pm, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
> Hi.
>
>
>
>
>
> On Tue, Jul 21, 2009 at 9:23 PM, Stellaw Chao<stellaw.c...@gmail.com> wrote:
>
> > Dear aroma.affymetrix developers,
> > I am a little bit confused while using ur package aroma.affymetrix to
> > process my dataset.
> > The following is my code——
>
> > setwd("C:/Array Files_CP2Bonly")
> > library("aroma.affymetrix")
> > cs <- AffymetrixCelSet$fromName("HapMap100K-bioc2007",
> > chipType="HG-U133_Plus_2")
> > qn <- QuantileNormalization(cs)
> > csQN <- process(qn, verbose=TRUE)
> > plm<-RmaCnPlm(csQN,combineAlleles=TRUE, mergeStrands=TRUE)
> > fit(plm, verbose=TRUE)
>
> > after the RmaCnPlm procedure, a set of new CEL Files(e.g.
> > "Mao101C075B,chipEffects" for an original CEL file "Mao101C075B") are
> > generated, yet I am not very clearly about the meaning of these new
> > Files, as their sizes are much smaller than the original ones (590KB
> > vs.13,225KB)
>
> They hold the summarized signals (in contrast to one per probe). You
> should access the signals in those files using extractMatrix(),
> extractTheta(), or extractDataFrame() which are available for single
> arrays (files) as well as sets of arrays (files), e.g.
>
> ces <- getChipEffectSet(plm);
>
> ce <- getFile(ces, 2);
> theta <- extractTheta(ce, units=1001:1012);
> theta <- extractTheta(ces, units=1001:1012);
>
> data <- extractDataFrame(ce, units=1001:1012, addNames=TRUE);
> data <- extractDataFrame(ces, units=1001:1012, addNames=TRUE);
>
> See also vignette:
>
> http://groups.google.com/group/aroma-affymetrix/web/calculating-raw-t...
>
> Unless you're a developer, consider those *,chipEffects.CEL files to
> be internal files of aroma.affymetrix. The details is that they only
> hold one cell ("probe") signal per unit group ("probeset"), which is
> also why they are smaller. They are read using the corresponding
> "monocell" CDF created automatically, e.g.
> HG-U133_Plus_2,monocell.cdf. See print(getCdf(ces)).
>
> /Henrik
>
>
>
>
>
> > Much Thanks for your help! Look forward to your reply!- Hide quoted text -
>
> - Show quoted text -- Hide quoted text -
>
> - Show quoted text -
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