Hi gouxiongpapa/felixli77quick, See below.
On Thu, Aug 5, 2010 at 9:33 AM, gouxiongpapa <felixli77qu...@gmail.com> wrote: > Hi there > > I wonder some one could kindly help me out from this: > > I am trying to process a data set of affy snp 250K sty, and I just > copied the steps in the vignette file: Estimation of total copy > numbers using the CRMA v2 method (10K-GWS6), as below > > > library(aroma.affymetrix) > cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Sty") > gi <- getGenomeInformation(cdf) > si <- getSnpInformation(cdf) > acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, > fullname=FALSE)) > csv <- AffymetrixNetAffxCsvFile$byChipType("Mapping250K_Sty", tag ="") > csR <- AffymetrixCelSet$fromFiles(path2[1], cdf=cdf) > acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2") > csC <- process(acc, verbose=verbose) > bpn <- BasePositionNormalization(csC, target="zero") > csN <- process(bpn, verbose=verbose) > plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE) Here you forgot fit(plm, verbose=TRUE) FYI this has been discussed several times on the list, see e.g. http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/6dfe3afc216f27fc/34442574ee1b039a Pierre > ces <- getChipEffectSet(plm) > fln <- FragmentLengthNormalization(ces, target="zero") > cesN <- process(fln, verbose=verbose) > > > !!!!!! > I got straight down here and got an error > Error in list(`process(fln, verbose = -1)` = <environment>, > `process.FragmentLengthNormalization(fln, verbose = -1)` = > <environment>, : > > [2010-08-05 12:22:33] Exception: Cannot fit normalization function to > enzyme, because there are no (finite) data points that are unique to > this enzyme: 1 > > I attached the entire screen below > !!!!! > ceR <- getAverageFile(cesN, verbose=verbose) > > > > > Normalizing set for PCR fragment-length effects... > Identifying SNP and CN units... > types > 2 > 238378 > subsetToUpdate: > int [1:238378] 1 2 3 4 5 6 7 8 9 10 ... > Identifying SNP and CN units...done > Retrieving SNP information annotations... > DChipSnpInformation: > Name: Mapping250K_Sty snp info > Tags: > Full name: Mapping250K_Sty snp info > Pathname: annotationData/chipTypes/Mapping250K_Sty/Mapping250K_Sty > snp info.txt > File size: 24.00 MB (25164292 bytes) > RAM: 17.28 MB > Chip type: Mapping250K_Sty > Number of enzymes: 1 > Retrieving SNP information annotations...done > Identifying the subset used to fit normalization function(s)... > int [1:233552] 1 2 3 4 5 6 7 8 9 10 ... > Identifying the subset used to fit normalization function(s)...done > Shift: 0 > onMissing: median > Array #1 of 49 > ('CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_A09_104500')... > V1 > Min. : 115 > 1st Qu.: 440 > Median : 598 > Mean : 609 > 3rd Qu.: 771 > Max. :1093 > NA's : 78 > int [1:233552] 1 2 3 4 5 6 7 8 9 10 ... > Getting cell matrix map... > 'UnitGroupCellMatrixMap' int [1:238378, 1] 1 2 3 4 5 6 7 8 9 > 10 ... > Getting cell matrix map...done > Getting theta estimates... > num [1:238378, 1] 0 0 0 0 0 0 0 0 0 0 ... > V1 > Min. :0 > 1st Qu.:0 > Median :0 > Mean :0 > 3rd Qu.:0 > Max. :0 > Getting theta estimates...done > Calculating total signals... > Total thetas: > num [1:238378] 0 0 0 0 0 0 0 0 0 0 ... > Calculating total signals...done > Normalizing log2 signals... > Log2 signals: > num [1:238378] -Inf -Inf -Inf -Inf -Inf ... > Error in list(`process(fln, verbose = -1)` = <environment>, > `process.FragmentLengthNormalization(fln, verbose = -1)` = > <environment>, : > > [2010-08-05 12:22:33] Exception: Cannot fit normalization function to > enzyme, because there are no (finite) data points that are unique to > this enzyme: 1 > at throw(Exception(...)) > at throw.default("Cannot fit normalization function to enzyme, > because there a > at throw("Cannot fit normalization function to enzyme, because there > are no (f > at normalizeFragmentLength.default(y, fragmentLengths = fl, > targetFcns = targe > at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns = > targetFcns, s > at process.FragmentLengthNormalization(fln, verbose = -1) > at process(fln, verbose = -1) > Normalizing log2 signals...done > Array #1 of 49 > ('CLONE_p_STY29_(CO-106422)_Mapping250K_Sty_A09_104500')...done > Normalizing set for PCR fragment-length effects...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 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. 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