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.
>
>
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>
--
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/.
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