Hi Henrik,
> sm <- CbsModel(ds2);
> cesTuple <- getSetTuple(sm);
> refTuple <- getReferenceSetTuple(sm);
> array <- 1L;
> ceList <- getFileList(cesTuple, array);
> rfList <- getFileList(refTuple, array);
> print(ceList);
$GenomeWideSNP_5
AromaUnitTotalCnBinaryFile:
Name: KMU20080903GRT1
Tags: total
Full name: KMU20080903GRT1,total
Pathname: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-
XY/GenomeWideSNP_5/KMU20080903GRT1,total.asb
File size: 3.51 MB (3684154 bytes)
RAM: 0.00 MB
Number of data rows: 920928
File format: v1
Dimensions: 920928x1
Column classes: double
Number of bytes per column: 4
Footer: <createdOn>20120120 20:14:43 CET</
createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_5</
chipType><srcFile><srcDataSet>Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A
+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_5,monocell</
srcChipType><srcFullName>KMU20080903GRT1,chipEffects</
srcFullName><srcChecksum>4675ac9f1da8fc9ed56c66c5cf0ba27c</
srcChecksum></srcFile>
Platform: Affymetrix
Chip type: GenomeWideSNP_5
attr(,"class")
[1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
[3] "list"
> print(rfList);
$`GenomeWideSNP_5,Full,r2`
AromaUnitTotalCnBinaryFile:
Name: .average-signals-median-mad
Tags: fb4e90561b3029ac7bc48d9aaad9b80e
Full name: .average-signals-median-
mad,fb4e90561b3029ac7bc48d9aaad9b80e
Pathname: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-
XY/GenomeWideSNP_5/.average-signals-median-
mad,fb4e90561b3029ac7bc48d9aaad9b80e.asb
File size: 3.51 MB (3684081 bytes)
RAM: 0.00 MB
Number of data rows: 920928
File format: v1
Dimensions: 920928x1
Column classes: double
Number of bytes per column: 4
Footer: <createdOn>20120121 14:24:19 CET</
createdOn><platform>Affymetrix</
platform><chipType>GenomeWideSNP_5,Full,r2</
chipType><srcDetails><nbrOfFiles>60</
nbrOfFiles><checkSum>45279a69a4857c4b7c13f6a7b6cd94a4</checkSum></
srcDetails><params><meanName>median</meanName><sdName>mad</sdName></
params>
Platform: Affymetrix
Chip type: GenomeWideSNP_5,Full,r2
attr(,"class")
[1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
[3] "list"
Thank you for your time!
Maxime
On Jan 24, 8:49 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi.
>
> this is odd, but there is for sure a simple explanation to it. Let's
> find out. I have my suspicions, but before moving to the next step,
> what does the following report:
>
> sm <- CbsModel(ds2);
> cesTuple <- getSetTuple(sm);
> refTuple <- getReferenceSetTuple(sm);
> array <- 1L;
> ceList <- getFileList(cesTuple, array);
> rfList <- getFileList(refTuple, array);
> print(ceList);
> print(rfList);
>
> /Henrik
>
> On Mon, Jan 23, 2012 at 1:52 AM, Maxime Tarabichi <galder....@gmail.com>
> wrote:
> > I hope this helps :
>
> >> traceback()
> > 8: throw.Exception(Exception(...))
> > 7: throw(Exception(...))
> > 6: throw.default("Internal error. Reference files of non-matching chip
> > types.")
> > 5: throw("Internal error. Reference files of non-matching chip
> > types.")
> > 4: getDataFileMatrix.CopyNumberChromosomalModel(this, array = array,
> > verbose = less(verbose, 5))
> > 3: getDataFileMatrix(this, array = array, verbose = less(verbose,
> > 5))
> > 2: fit.CopyNumberSegmentationModel(sm, verbose = -10)
> > 1: fit(sm, verbose = -10)
>
> >> fit(sm, verbose=-10)
> > Building tuple of reference sets...
> > No reference available.
> > Calculating average copy-number signals...
> > Retrieving average unit signals across 60 arrays...
> > Searching for an existing file...
> > Paths:
> > [1] "totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-
> > XY/GenomeWideSNP_5"
> > Filename: .average-signals-median-
> > mad,fb4e90561b3029ac7bc48d9aaad9b80e.asb
> > Searching path #1 of 1...
> > Path: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-
> > XY/GenomeWideSNP_5
> > Pathname: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A
> > +B,FLN,-XY/GenomeWideSNP_5/.average-signals-median-
> > mad,fb4e90561b3029ac7bc48d9aaad9b80e.asb
> > Found an existing file.
> > Searching path #1 of 1...done
> > Located pathname: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5/.average-signals-median-
> > mad,fb4e90561b3029ac7bc48d9aaad9b80e.asb
> > Searching for an existing file...done
> > Loading existing data file...
> > Loading existing data file...done
> > AromaUnitTotalCnBinaryFile:
> > Name: .average-signals-median-mad
> > Tags: fb4e90561b3029ac7bc48d9aaad9b80e
> > Full name: .average-signals-median-
> > mad,fb4e90561b3029ac7bc48d9aaad9b80e
> > Pathname: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A
> > +B,FLN,-XY/GenomeWideSNP_5/.average-signals-median-
> > mad,fb4e90561b3029ac7bc48d9aaad9b80e.asb
> > File size: 3.51 MB (3684081 bytes)
> > RAM: 0.00 MB
> > Number of data rows: 920928
> > File format: v1
> > Dimensions: 920928x1
> > Column classes: double
> > Number of bytes per column: 4
> > Footer: <createdOn>20120121 14:24:19 CET</
> > createdOn><platform>Affymetrix</
> > platform><chipType>GenomeWideSNP_5,Full,r2</
> > chipType><srcDetails><nbrOfFiles>60</
> > nbrOfFiles><checkSum>45279a69a4857c4b7c13f6a7b6cd94a4</checkSum></
> > srcDetails><params><meanName>median</meanName><sdName>mad</sdName></
> > params>
> > Platform: Affymetrix
> > Chip type: GenomeWideSNP_5,Full,r2
> > Retrieving average unit signals across 60 arrays...done
> > Calculating average copy-number signals...done
> > Building tuple of reference sets...done
> > Using reference tuple:
> > AromaUnitTotalCnBinarySetTuple:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Chip types: GenomeWideSNP_5
> > AromaUnitTotalCnBinarySet:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Full name: Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Number of files: 60
> > Names: .average-signals-median-mad, .average-signals-median-
> > mad, .average-signals-median-mad, ..., .average-signals-median-mad
> > [60]
> > Path (to the first file): totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5
> > Total file size: 210.80 MB
> > RAM: 0.07MB
> > RAM: 0.00MB
> > Extract DataFileMatrix...
> > Array: 1
> > Test data sets:
> > AromaUnitTotalCnBinarySetTuple:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Chip types: GenomeWideSNP_5
> > AromaUnitTotalCnBinarySet:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Full name: Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Number of files: 60
> > Names: KMU20080903GRT1, KMU20080903GRT2, KMU20080903GRT3, ...,
> > UA991N_181208 [60]
> > Path (to the first file): totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5
> > Total file size: 210.81 MB
> > RAM: 0.07MB
> > RAM: 0.00MB
> > Reference data sets:
> > AromaUnitTotalCnBinarySetTuple:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Chip types: GenomeWideSNP_5
> > AromaUnitTotalCnBinarySet:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Full name: Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Number of files: 60
> > Names: .average-signals-median-mad, .average-signals-median-
> > mad, .average-signals-median-mad, ..., .average-signals-median-mad
> > [60]
> > Path (to the first file): totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5
> > Total file size: 210.80 MB
> > RAM: 0.07MB
> > RAM: 0.00MB
> > Test data files:
> > $GenomeWideSNP_5
> > AromaUnitTotalCnBinaryFile:
> > Name: KMU20080903GRT1
> > Tags: total
> > Full name: KMU20080903GRT1,total
> > Pathname: totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-
> > XY/GenomeWideSNP_5/KMU20080903GRT1,total.asb
> > File size: 3.51 MB (3684154 bytes)
> > RAM: 0.00 MB
> > Number of data rows: 920928
> > File format: v1
> > Dimensions: 920928x1
> > Column classes: double
> > Number of bytes per column: 4
> > Footer: <createdOn>20120120 20:14:43 CET</
> > createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_5</
> > chipType><srcFile><srcDataSet>Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A
> > +B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_5,monocell</
> > srcChipType><srcFullName>KMU20080903GRT1,chipEffects</
> > srcFullName><srcChecksum>4675ac9f1da8fc9ed56c66c5cf0ba27c</
> > srcChecksum></srcFile>
> > Platform: Affymetrix
> > Chip type: GenomeWideSNP_5
>
> > attr(,"class")
> > [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> > [3] "list"
> > Error in list(`fit(sm, verbose = -10)` = <environment>,
> > `fit.CopyNumberSegmentationModel(sm, verbose = -10)` =
> > <environment>, :
>
> > [2012-01-23 10:38:35] Exception: Internal error. Reference files of
> > non-matching chip types.
> > at throw(Exception(...))
> > at throw.default("Internal error. Reference files of non-matching
> > chip types."
> > at throw("Internal error. Reference files of non-matching chip
> > types.")
> > at getDataFileMatrix.CopyNumberChromosomalModel(this, array = array,
> > verbose =
> > at getDataFileMatrix(this, array = array, verbose = less(verbose,
> > 5))
> > at fit.CopyNumberSegmentationModel(sm, verbose = -10)
> > at fit(sm, verbose = -10)
> > Extract DataFileMatrix...done
>
> >> print(ds2)
> > AromaUnitTotalCnBinarySet:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Full name: Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Number of files: 60
> > Names: KMU20080903GRT1, KMU20080903GRT2, KMU20080903GRT3, ...,
> > UA991N_181208 [60]
> > Path (to the first file): totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5
> > Total file size: 210.81 MB
> > RAM: 0.07MB
>
> >> print(table(sapply(ds2, getChipType)))
>
> > GenomeWideSNP_5
> > 60
>
> >> cesTuple <- getSetTuple(sm); print(cesTuple);
> > AromaUnitTotalCnBinarySetTuple:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Chip types: GenomeWideSNP_5
> > AromaUnitTotalCnBinarySet:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Full name: Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Number of files: 60
> > Names: KMU20080903GRT1, KMU20080903GRT2, KMU20080903GRT3, ...,
> > UA991N_181208 [60]
> > Path (to the first file): totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5
> > Total file size: 210.81 MB
> > RAM: 0.07MB
> > RAM: 0.00MB
>
> >> refTuple <- getReferenceSetTuple(sm); print(refTuple);
> > AromaUnitTotalCnBinarySetTuple:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Chip types: GenomeWideSNP_5
> > AromaUnitTotalCnBinarySet:
> > Name: Chernobyl
> > Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Full name: Chernobyl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> > Number of files: 60
> > Names: .average-signals-median-mad, .average-signals-median-
> > mad, .average-signals-median-mad, ..., .average-signals-median-mad
> > [60]
> > Path (to the first file): totalAndFracBData/Chernobyl,ACC,ra,-XY,BPN,-
> > XY,AVG,A+B,FLN,-XY/GenomeWideSNP_5
> > Total file size: 210.80 MB
> > RAM: 0.07MB
> > RAM: 0.00MB
>
> > Maxime
>
> > On Jan 21, 10:04 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> > project.org> wrote:
> >> Hi.
>
> >> On Sat, Jan 21, 2012 at 10:29 AM, Maxime Tarabichi <galder....@gmail.com>
> >> wrote:
> >> > Hi Henrik, thanks for the quick reply!
>
> >> > In fact, I had installed the aroma.affymetrix package the day before
> >> > my post with :
> >> > source("http://aroma-project.org/hbLite.R";);
> >> > hbInstall("aroma.affymetrix");
> >> > Yesterday I installed the latest version of R and tried again : I now
> >> > have the aroma.affymetrix_2.4.0.
>
> >> Good. That will make troubleshooting possible.
>
> >> > I ran my code again from scratch but ended up with the initial
> >> > problem : "Exception: Internal error. Reference files of non-matching
> >> > chip types" in the fit(CbsModel) function.
>
> >> This error occurs because an internal sanity check detected that
> >> different chip type *labels* have been used. I never seen this
> >> before; it may or may not be a bug.
>
> >> So, a few things helps troubleshooting:
>
> >> 1. The stack trace reported together with the error.
>
> >> 2. The verbose output lines ~10-20 lines before the error occurs.
>
> >> 3. Result of print(ds2);
>
> >> 4. Result of print(sapply(ds2, getChipType)); If too many files, use
> >> print(table(sapply(ds2, getChipType)));
>
> >> 5. cesTuple <- getSetTuple(sm); print(cesTuple);
>
> >> 6.
>
> ...
>
> read more »
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