Hi Hailei. For starters, can you give the *full* output of your sessionInfo()? The error you are getting has something to do with the 'preprocessCore' package and I first want to check whether it is a package version mismatch error.
I haven't used aroma.affymetrix on R 2.10 and I don't know if anyone else has either. You could try all this on R 2.9.2 ... Cheers, Mark > > Dear All, > > I am analyzing human affy exon arrays for first time. I followed the > steps listed in website: > http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis > > In summarization step, I met an error when I began to fit the PLM to > all of the data. > > Thanks > Hailei > > > my R session: >> sessionInfo() > R version 2.10.0 Under development (unstable) (2009-08-10 r49148) > x86_64-unknown-linux-gnu > > My script: > library(aroma.affymetrix) > verbose <- Arguments$getVerbose(-8,timestamp=TRUE) > chipType <- "HuEx-1_0-st-v2" > cdf <- AffymetrixCdfFile$byChipType(chipType, > tags="coreR3,A20071112,EP") > print(cdf) > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) > print(cs) > bc <- RmaBackgroundCorrection(cs, tag="coreR3") > csBC <- process(bc,verbose=verbose) > qn <- QuantileNormalization(csBC, typesToUpdate="pm") > print(qn) > csN <- process(qn, verbose=verbose) > plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) > print(plmTr) > fit(plmTr,verbose=verbose) > > The error is: > >> fit(plmTr, verbose=verbose) > 20091015 15:49:54|Fitting model of class ExonRmaPlm:... > ExonRmaPlm: > Data set: tissues > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP > Input tags: coreR3,QN > Output tags: coreR3,QN,RMA,merged > Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr > "affyPLM"; treatNAsAs: chr "weights"; mergeGroups: logi TRUE). > Path: plmData/tissues,coreR3,QN,RMA,merged/HuEx-1_0-st-v2 > RAM: 0.01MB > 20091015 15:49:54| Identifying non-estimated units... > 20091015 15:49:54| Identifying non-fitted units in chip-effect > file... > 20091015 15:49:54| Pathname: plmData/tissues,coreR3,QN,RMA,merged/ > HuEx-1_0-st-v2/RD2009092837,chipEffects.CEL > 20091015 15:49:54| Found indices cached on file > 20091015 15:49:54| Reading data for these 18708 cells... > 20091015 15:49:54| Reading data for these 18708 cells...done > 20091015 15:49:54| Looking for stdvs <= 0 indicating non-estimated > units: > int [1:18708] 1 2 3 4 5 6 7 8 9 10 ... > 20091015 15:49:54| Identifying non-fitted units in chip-effect > file...done > 20091015 15:49:54| Identifying non-estimated units...done > 20091015 15:49:54| Getting model fit for 18708 units. > <simpleError in .Call("R_rlm_rma_default_model", y, psiCode, psiK, > PACKAGE = rlmPkg): Incorrect number of arguments (3), expecting 4 for > R_rlm_rma_default_model> > Error in list(`fit(plmTr, verbose = verbose)` = <environment>, > `fit.ProbeLevelModel(plmTr, verbose = verbose)` = <environment>, : > > [2009-10-15 15:49:54] Exception: The fit function for requested exon > RMA PLM failed > at throw(Exception(...)) > at throw.default("The fit function for requested exon RMA PLM > failed") > at throw("The fit function for requested exon RMA PLM failed") > at getFitUnitGroupFunction.ExonRmaPlm(this, ...) > at getFitUnitGroupFunction(this, ...) > at getFitUnitFunction.MultiArrayUnitModel(this) > at getFitUnitFunction(this) > at fit.ProbeLevelModel(plmTr, verbose = verbose) > at fit(plmTr, verbose = verbose) > 20091015 15:49:54|Fitting model of class ExonRmaPlm:...done > > > > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
