Thank you!!
On 10月23日, 上午1时55分, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi > > On Fri, Oct 21, 2011 at 8:17 PM, marco <hardstar...@gmail.com> wrote: > > Thanks a lot!! > > Yes,i did the same job previously. > > How does aroma.affymetrix make the result "persistent" and > > "memorized"? > > FYI, it is indeed "memoized" (without "r"), cf. the R.cache package > andhttp://en.wikipedia.org/wiki/Memoization > > > Are such results stored in disk files like .RData? > > Mostly it stores intermediate results as CEL files, but yes, some are > binary R data files, especially the memoized results. For more > details see: > > H. Bengtsson, K. Simpson, J. Bullard & K. Hansen, aroma.affymetrix: A > generic framework in R for analyzing small to very large Affymetrix > data sets in bounded memory, Tech Report #745, Department of > Statistics, University of California, Berkeley, February 2008. > Download:http://aroma-project.org/publications/ > > The following may also do be useful: > > http://aroma-project.org/howtos/DeleteIntermediateDataFilesWhileKeepi...http://aroma-project.org/howtos/MigrateAndReproduceAnAnalysisElsewhere > > > Does it matter If i restart the computer? > > No. You can force processing by using argument 'force=TRUE' in the > calls to process() and fit(). Alternatively, you can just delete the > directory that contains the result files you wish to redo. > > /Henrik > > > > > > > > > > > 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 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/ -- 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/
