[aroma.affymetrix] Cannot fit normalization function to enzyme, because there are no (finite) data points that are unique to this enzyme: 1

[gouxiongpapa]

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)
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

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