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 and http://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/DeleteIntermediateDataFilesWhileKeepingFinalOnes 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 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/ > -- 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/
