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. > > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/- > > 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/