Thanks a lot!!
Yes,i did the same job previously.
How does aroma.affymetrix make the result "persistent" and
"memorized"?
Are such results stored in disk files like .RData?
Does it matter If i restart the computer?
On Oct 21, 11:24 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi.
>
> On Fri, Oct 21, 2011 at 8:15 AM, marco <hardstar...@gmail.com> wrote:
> > Hello Henrik and everyone else
> > I currently run RMA in aroma.affymetrix on dataset GSE21034 which
> > contains 179 human exon 1.0 ST arrays. i use a custom CDF,
> > huex10stv2hsrefseqcdt, from brainarray. the resulting data matrix
> > contains 42667 rows.What supprised me is the whole processing finished
> > in just a few minutes!
> > Is it possible to finish jobs like this in such a short time? i am
> > afraid that i did not realise some coding mistakes. Below is my code.
>
> It will finish within minutes, if you have previously ran the same
> steps. All final and intermediate results in Aroma Framework are
> "persistent" and "memoized", which means that if they already exists
> and you call the same method with the same input the result will be
> retrieved quickly (from file).
>
> If it finishes within minutes and you haven't processed the data
> previously, then yes, it sound suspicious and most likely there is an
> error, e.g. incorrect/very small annotation data.
>
> /Henrik
>
>
>
> > Thanks a lot!!
>
> > library(aroma.affymetrix)
> > cdf <- AffymetrixCdfFile
> > $byChipType("HuEx10stv2_Hs_REFSEQ",tags="20110928")
> > cs <- AffymetrixCelSet$byName("GSE21034_179",cdf=cdf)
> > bc <- RmaBackgroundCorrection(cs,tag="20110928")
> > date();csBC <- process(bc);date()
> > date();qn <- QuantileNormalization(csBC,typesToUpdate="pm");date()
> > date();csN <- process(qn);date()
> > date();plmTr <- ExonRmaPlm(csN,mergeGroups=TRUE);date()
> > date();fit(plmTr);date()
> > cesTr <- getChipEffectSet(plmTr)
> > trFit <- extractDataFrame(cesTr,unit=NULL,addNames=TRUE)
>
> > --
> > 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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> > Hide quoted text -
>
> - Show quoted text -
--
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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