Hi. On Mon, Jan 30, 2012 at 11:45 PM, Maxime Tarabichi <galder....@gmail.com> wrote: > Hi, > > sorry for replying only now. > Indeed I renamed them. I removed the tags they had on the > aroma.affymetrix website.
Ok, that explains everything. So, never do that; tags are there for a reason. A rule of thumb that I found useful when it comes to R is: "If you find yourself having to do ad hoc tricks to get around a problem/error message, it is likely you are doing something you shouldn't do. Instead ask for advice." That also applies when using the Aroma Framework [ ...and probably life in general ;) ] > > print(fi); > GenomeWideSNP_5,monocell.CDF GenomeWideSNP_5.acs > 218402031 121981027 > GenomeWideSNP_5.cdf GenomeWideSNP_5.ufl > 261578689 3684511 > GenomeWideSNP_5.ugp > 4605439 > > What should I do instead? Two things: (1) UPDATE/CORRECT annotationData/chipTypes/GenomeWideSNP_5/ files: (a) You can keep the following but you have to add those tags back that you dropped: - GenomeWideSNP_5,HB20080710.acs [121981027 bytes] - GenomeWideSNP_5,Full,r2,na26,HB20080822.ufl [3684511 bytes] - GenomeWideSNP_5,Full,r2,na26,HB20080822.ugp [4605439 bytes] If their filesizes are not exactly as that, just delete them and download them again (and unzip). (b) Then you need to rename the CDF you have to: - GenomeWideSNP_5,Full,r2.cdf [261578689 bytes] FYI, for GenomeWideSNP_5 and GenomeWideSNP_6 Affymetrix provides a "default" and a "full" CDF (they stopped doing that in newer chip types), which makes things a little bit confusing. It is explained in http://aroma-project.org/chipTypes/GenomeWideSNP_5. Then they also have a revision 2 tag ("r2"), which adds to more confusion. The only annotation data file that does not have to have the "Full" and the "r2" tags is the ACS (which contains the probe sequences and hence never ever change regardless of human genome annotations). (c) You also need to delete the GenomeWideSNP_5,monocell.CDF [218402031 bytes] file. (2) VERIFY that you've got the above correctly Start a fresh R session and do: library("aroma.affymetrix"); cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_5", tags="Full,r2"); print(cdf); stopifnot(identical(getChecksum(cdf), "79f7a8353b4978dedbeff05a7897ff6e")); acs <- getAromaCellSequenceFile(cdf); print(acs); stopifnot(identical(getChecksum(acs), "bd0da64b09ea164082e066798774a3c5")); ugp <- getAromaUgpFile(cdf); print(ugp); stopifnot(identical(getChecksum(ugp), "9827c9fad08144d6e590b87984350a26")); ufl <- getAromaUflFile(cdf); print(ufl); stopifnot(identical(getChecksum(ufl), "a533ac3ba64f36902d13bed8fe2a9a5b")); If any of these gives an error, let me know. (3) CLEANUP/REMOVE the previous analysis because it is invalid: Delete all subdirectories in probeData/, plmData/, and totalAndFracBData/ (and possibly also rawCnData/ and cbsData/ if they exists), e.g. probeData/Chernobyl,ACC,ra,-XY/, probeData/Chernobyl,ACC,ra,-XY,BPN,-XY/ and so on. You should not have any subdirectories floating around related to the Chernobyl dataset, *except* of course keeping your raw data in rawData/Chernobyl/. (4) PREPROCESS YOUR DATA USING: library("aroma.affymetrix"); cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_5", tags="Full,r2"); csR <- AffymetrixCelSet$byName("Chernobyl", cdf=cdf); print(csR); ds <- doCRMAv2(csR, verbose=-10); print(ds); sm <- CbsModel(ds); print(sm); fit(sm, verbose=-10); Let me know how it goes. /Henrik PS. We try our best to have aroma detect these types of user mistakes, but here we failed. I'll see if I can add further protection against this. > > Thanks, > > Maxime > > > On Jan 25, 11:45 am, Henrik Bengtsson <henrik.bengts...@aroma- > project.org> wrote: >> Hi, >> >> my guess is that you've don't have the correct annotation data files. >> For instance, could it be that you had to rename the UGP and UFL files >> in order to get doCRMAv2() to run? What does the following give? >> >> library("R.utils"); >> path <- "annotationData/chipTypes/GenomeWideSNP_5/"; >> path <- Arguments$getReadablePath(path); >> filenames <- list.files(path=path, full.names=FALSE); >> fi <- sapply(filenames, FUN=function(filename) { >> file.info(file.path(path, filename))$size;}); >> >> print(fi); >> >> /Henrik >> >> On Wed, Jan 25, 2012 at 2:07 AM, Maxime Tarabichi <galder....@gmail.com> >> wrote: >> > 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. >> >> ... >> >> read more » > > -- > 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/
