Hello, I am stuck trying to run the script:
options(echo = FALSE,digits=4)
library(aroma.affymetrix)
verbose <- Verbose(threshold=-8, timestamp=TRUE);
name="pediatric_HGG"
chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty")
cesNList <- list()
for(chipType in chipTypes) {
dsList <- doCRMAv2(name, chipType=chipType,
combineAlleles=FALSE, verbose=verbose,plm="RmaCnPlm");
cesNList[[chipType]] <- dsList$total;
}
glad <- GladModel(cesNList)
fit(glad)
ce <- ChromosomeExplorer(glad)
process(ce, verbose=verbose)
and it crushes with :
.....
20111031 15:28:33| Processing chunk...done
20111031 15:28:33| Retrieving average unit signals across 121 arrays...done
20111031 15:28:33| Calculating average copy-number signals...done
20111031 15:28:33| No reference available.
20111031 15:28:33| Calculating average copy-number signals...
20111031 15:28:33| Retrieving average unit signals across 121 arrays...
AromaUnitTotalCnBinaryFile:
Name: .average-signals-median-mad
Tags: c3edea4f9b61fd7facd34e7a80921726
Full name: .average-signals-median-mad,c3edea4f9b61fd7facd34e7a80921726
Pathname:
totalAndFracBData/pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Sty/.average-signals-median-mad,c3edea4f9b61fd7facd34e7a80921726.asb
File size: 931.52 kB (953874 bytes)
RAM: 0.00 MB
Number of data rows: 238378
File format: v1
Dimensions: 238378x1
Column classes: double
Number of bytes per column: 4
Footer: <createdOn>20111028 23:51:40
PDT</createdOn><platform>Affymetrix</platform><chipType>Mapping250K_Sty</chipType><srcDetails><nbrOfFiles>121</nbrOfFiles><checkSum>38ca3ec6eb1bd5507526ca152d6a6cc7</checkSum></srcDetails><params><meanName>median</meanName><sdName>mad</sdName></params>
Platform: Affymetrix
Chip type: Mapping250K_Sty
20111031 15:28:33| Number of units to be updated: 6
20111031 15:28:33| Processing chunk...
chr "Indices in chunk:"
int [1:6] 39 45 52 60 79779 168680
20111031 15:28:33| Reading data...
20111031 15:28:34| Reading data...done
20111031 15:28:34| Estimating averages and standard deviations...
20111031 15:28:34| Estimating averages and standard deviations...done
20111031 15:28:34| Writing estimates...
20111031 15:28:34| Writing estimates...done
20111031 15:28:34| Processing chunk...done
20111031 15:28:34| Retrieving average unit signals across 121 arrays...done
20111031 15:28:35| Calculating average copy-number signals...done
20111031 15:28:35| Building tuple of reference sets...done
20111031 15:28:35| Using reference tuple:
Error in list(`process(ce, verbose = verbose)` = <environment>,
`process.ChromosomeExplorer(ce, verbose = verbose)` = <environment>,
:
[2011-10-31 15:28:35] Exception: Argument 'x' is of length 1 although
the range ([0,0]) implies that is should be empty.
at throw(Exception(...))
at throw.default(sprintf("Argument 'x' is of length %d although the range ([%s
at throw(sprintf("Argument 'x' is of length %d although the range ([%s,%s]) im
at getIndices.Arguments(static, ..., length = length)
at getIndices(static, ..., length = length)
at method(static, ...)
at Arguments$getIndex(idx, max = n)
at getFile.GenericDataFileSet(this, 1)
at getFile(this, 1)
at getChipType(getFile(this, 1), ...)
at getChipType.AromaUnitSignalBinarySet(X[[1]], ...)
at FUN(X[[1]], ...)
at lapply(X, FUN, ...)
at sapply.default(res, FUN = getChipType)
at sapply(res, FUN = getChipType)
at getSets.AromaMicroarrayDataSetTuple(this)
at getSets(this)
at getDefaultFullName.GenericDataFileSetList(this, ...)
at getDefaultFullName(this, ...)
at getFullName.FullNameInterface(this, ...)
at getFullName(this, .
Calls: process ... getIndices.Arguments -> throw -> throw.default ->
throw -> throw.Exception
20111031 15:28:35|Generating ChromosomeExplorer report...done
Execution halted
Same thing with CBS model. Annotation files seem to be OK...
Help!
Ivan
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