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. refTuple <- getReferenceSetTuple(sm); print(refTuple);
>>
>> /Henrik
>>
>>
>>
>> > What am I doing wrong?
>>
>> > On Jan 20, 3:57 am, Henrik Bengtsson <henrik.bengts...@aroma-
>> > project.org> wrote:
>> >> You need to update aroma.affymetrix. The version you are using is
>> >> from July 2010.
>>
>> >> Thanks for the note about sfit and 64-bit machines. I'll add it to the
>> >> list of things to look at.
>>
>> >> /Henrik
>>
>> >> On Thu, Jan 19, 2012 at 2:48 AM, Maxime Tarabichi <galder....@gmail.com>
>> >> wrote:
>> >> > Hi,
>>
>> >> > I have a problem when segmenting after successfully running doCRMAv2().
>> >> > Here
>> >> > it is :
>> >> > sessionInfo()
>> >> > R version 2.11.1 (2010-05-31)
>> >> > i386-apple-darwin9.8.0
>>
>> >> > locale:
>> >> > [1] C
>>
>> >> > attached base packages:
>> >> > [1] stats graphics grDevices utils datasets methods base
>>
>> >> > other attached packages:
>> >> > [1] GLAD_2.10.0 DNAcopy_1.22.1 sfit_0.2.0
>> >> > aroma.affymetrix_1.7.0 affxparser_1.20.0 aroma.apd_0.2.0
>> >> > R.huge_0.3.0 aroma.core_1.9.1
>> >> > [9] aroma.light_1.22.0 matrixStats_0.2.2 R.rsp_0.7.1
>> >> > R.filesets_0.9.1 digest_0.4.2 R.cache_0.5.2
>> >> > R.utils_1.9.11 R.oo_1.8.3
>> >> > [17] R.methodsS3_1.2.1
>>
>> >> > loaded via a namespace (and not attached):
>> >> > [1] splines_2.11.1 tools_2.11.1
>>
>> >> > 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(gd)
>> >> > 1: fit(gd)
>>
>> >> > And my code looks like this :
>>
>> >> > library(aroma.affymetrix)
>> >> > setwd("/Users/Maxime/Desktop/SNPCRMA/")
>> >> > ds <- doCRMAv2("Chernobyl", chipType="GenomeWideSNP_5")
>> >> > dataSet <- "Chernobyl"
>> >> > tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"
>> >> > chipType <- "GenomeWideSNP_5"
>> >> > ds2 <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
>> >> > chipType=chipType)
>> >> > sm <- CbsModel(ds2)
>> >> > fit(sm, verbose=-10)
>>
>> >> > Error is located here :
>> >> > getDataFileMatrix.CopyNumberChromosomalModel
>> >> > function (this, array, ..., verbose = FALSE)
>> >> > {
>> >> > ...
>> >> > if (!identical(names(ceList), names(rfList)))
>> >> > throw("Internal error. Reference files of non-matching chip
>> >> > types.")
>> >> > ...
>> >> > }
>>
>> >> > What could it be?
>>
>> >> > By the way, I use R 32 bits because for some reason, I could not source
>> >> > all
>> >> > the packages needed with the 64 bits version notably : sfit, which is
>> >> > absolutely necessary. On another Snow Leopard R64 with a more recent
>> >> > version of R, the installs worked fine but I had an abort trap problem
>> >> > when
>> >> > doing doCRMAv2() (I think when loading the cdf file...)
>> >> > I have seen similar problems in other posts and it seems unrelated to
>> >> > aroma.affymetrix. But I felt like sharing here because this is weird!
>>
>> >> > Thanks for your help!
>>
>> >> > Maxime
>>
>> >> > --
>> >> > 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 websitehttp://www.aroma-project.org/.
>> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> >> > To unsubscribe and other options, go
>> >> > tohttp://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.
>>
>> > You received this message because you are subscribed to the Google Groups
>> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://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.
>
>
> 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.
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/
