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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--
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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