[aroma.affymetrix] Problem with Total Copy Number Vignette
Hello, I sent an e-mail earlier regarding errors in running the total copy number vignette, but please disregard that as it turns out it was just an issue with the annotation files. Sorry for the inconveniences. However, I've encountered another problem that I'm hoping someone could help me with. After running the normalization of the chip effects using: cesNList[[chipType]] - process(fln, verbose=verbose) I encountered the error of: Error in list(`process(fln, verbose = verbose)` = environment, `process.FragmentLengthNormalization(fln, verbose = verbose)` = environment, : [2010-06-07 09:34:07] Exception: Cannot fit target function to enzyme, because there are no (finite) data points that are unique to this enzyme: 1 sessionInfo() R version 2.11.1 (2010-05-31) powerpc-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_1.6.0 aroma.apd_0.1.7affxparser_1.20.0 R.huge_0.2.0 aroma.core_1.6.0 [6] aroma.light_1.16.0 matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.1 [11] digest_0.4.2 R.utils_1.4.0 R.oo_1.7.2 R.methodsS3_1.2.0 traceback() 8: throw.Exception(Exception(...)) 7: throw(Exception(...)) 6: throw.default(Cannot fit target function to enzyme, because there are no (finite) data points that are unique to this enzyme: , ee) 5: throw(Cannot fit target function to enzyme, because there are no (finite) data points that are unique to this enzyme: , ee) 4: getTargetFunctions.FragmentLengthNormalization(this, verbose = less(verbose)) 3: getTargetFunctions(this, verbose = less(verbose)) 2: process.FragmentLengthNormalization(fln, verbose = verbose) 1: process(fln, verbose = verbose) Thanks in advance, Jack -- Jack Y. Yu Washington University in St.Louis (505) 920-0701 -- 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/
[aroma.affymetrix] Re: Error during Total copy number analysis using CRMA v1
Hi Henrik, Yes that is correct, sorry again for the inconveniences. Jack On Jun 7, 12:12 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote: Hi Jack, from your new message '[aroma.affymetrix] Problem with Total Copy Number Vignette': On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu j.yu...@gmail.com wrote: Hello, I sent an e-mail earlier regarding errors in running the total copy number vignette, but please disregard that as it turns out it was just an issue with the annotation files. Sorry for the inconveniences. URL:http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/... I conclude that you have solved the issue regarding the monocell CDF discussed in this thread. /Henrik On Sat, Jun 5, 2010 at 4:54 PM, Henrik Bengtsson h...@stat.berkeley.edu wrote: Hi Jack. On Fri, Jun 4, 2010 at 7:43 PM, Jack kangarooj...@gmail.com wrote: Hi all, Let me preface this by saying I'm an introductory user when it comes to R. I have a list of massive CEL files and I need to obtain the copy numbers from them. The error message I've encountered when using the vignette (http://www.aroma-project.org/vignettes/CRMAv1) is from the function fit(plm, verbose=verbose), after the Summerization step. The error, I believe, has to do with the subsequent creation of the file GenomeWideSNP_6,Full,monocell.CDF.tmp, with GenomeWideSNP_6,Full.cdf being the cdf file used. Correct. When aroma does probe-level summarization, a so called monocell CDF is needed. It is created automatically (from the main CDF) and only once per life time of a new chip type/CDF, cf. http://aroma-project.org/FAQ/ As the below traceback shows, fit() will call getMonocellCdf(cdf) internally. So, you can reproduce this error simply by calling this directly. I have verified that it works on our test servers, so my best guess is that the CDF you've downloaded is not correct. To troubleshoot, do the following and assert that you have the same file/output: library(aroma.affymetrix); cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full); print(cdf); AffymetrixCdfFile: Path: annotationData/chipTypes/GenomeWideSNP_6 Filename: GenomeWideSNP_6,Full.CDF Filesize: 470.44MB Chip type: GenomeWideSNP_6,Full RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 print(getChecksum(cdf)); [1] 3fbe0f6e7c8a346105238a3f3d10d4ec If you get a different output, the let me know verbatim what you get. If you get the identical output, let's continue by first deleting the 'GenomeWideSNP_6,Full,monocell.CDF.tmp' file. Then, do: verbose - Arguments$getVerbose(-8, timestamp=TRUE); cdfM - getMonocellCdf(cdf, verbose=verbose); you should see something like this: 20100605 06:54:00|Retrieving monocell CDF... 20100605 06:54:00| Monocell chip type: GenomeWideSNP_6,Full,monocell 20100605 06:54:00| Locating monocell CDF... 20100605 06:54:00| Pathname: 20100605 06:54:00| Locating monocell CDF...done 20100605 06:54:00| Could not locate monocell CDF. Will create one for chip type... 20100605 06:54:00| Creating monocell CDF... 20100605 06:54:00| Chip type: GenomeWideSNP_6,Full 20100605 06:54:00| Output pathname (temporary): annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,monocell.CDF. tmp 20100605 06:54:00| Number of cells per group field: 1 20100605 06:54:00| Reading CDF group names... [...] 20100605 06:55:50| Argument 'ram': 1.00 20100605 06:55:50| Average unit length: 163.987575 bytes 20100605 06:55:50| Number of chunks: 78 (24392 units/chunk) 20100605 06:55:50| Reading, extracting, and writing units... 20100605 06:55:50| Chunk #1 of 78 (24392 units) 20100605 06:55:50| Reading CDF list structure... 20100605 06:55:51| Reading CDF list structure...done = RAM: 107MB Writes 24392 units... Units left: 23392, 22392, 21392, 20392, 19392, 18392, 17392, 16392, 15392, 14392, 13392, 12392, 11392, 10392, 9392, 8392, 7392, 6392, 5392, 4392, 3392, 2392, 1392, 392, 0 Writes 24392 units...done 20100605 06:56:26| Chunk #2 of 78 (24392 units) 20100605 06:56:26| Reading CDF list structure... 20100605 06:56:27| Reading CDF list structure...done = RAM: 107MB Writes 24392 units... [...] Writes 24392 units... Units left: 23392, 22392, 21392, 20392, 19392, 18392, 17392, 16392, 15392, 14392, 13392, 12392, 11392, 10392, 9392, 8392, 7392, 6392, 5392, 4392, 3392, 2392, 1392, 392, 0 Writes 24392 units...done 20100605 07:49:07| Chunk #78 of 78 (3231 units) 20100605 07:49:07| Reading CDF list structure... 20100605 07:49:08| Reading CDF list structure...done = RAM: 9MB Writes 3231 units... Units left: 2231, 1231, 231, 0 Writes 3231 units...done used (Mb) gc trigger (Mb) max used (Mb) Ncells
[aroma.affymetrix] Re: Problem with Total Copy Number Vignette
Hi Henrik, I've ran the entirety of the vignette up to the same point (I did forget to run the fit(plm, verbose=verbose) and the same error persists. The reason I'm using version 1 is because all we need is the raw copy number so we didn't need any of the additional tools/calculations. traceback() 8: throw.Exception(Exception(...)) 7: throw(Exception(...)) 6: throw.default(Cannot fit target function to enzyme, because there are no (finite) data points that are unique to this enzyme: , ee) 5: throw(Cannot fit target function to enzyme, because there are no (finite) data points that are unique to this enzyme: , ee) 4: getTargetFunctions.FragmentLengthNormalization(this, verbose = less(verbose)) 3: getTargetFunctions(this, verbose = less(verbose)) 2: process.FragmentLengthNormalization(fln, verbose = verbose) 1: process(fln, verbose = verbose) sessionInfo() R version 2.11.1 (2010-05-31) powerpc-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.10.0 aroma.affymetrix_1.6.0 aroma.apd_0.1.7affxparser_1.20.0 R.huge_0.2.0 [6] aroma.core_1.6.0 aroma.light_1.16.0 matrixStats_0.2.1 R.rsp_0.3.6R.cache_0.3.0 [11] R.filesets_0.8.1 digest_0.4.2 R.utils_1.4.0 R.oo_1.7.2 R.methodsS3_1.2.0 loaded via a namespace (and not attached): [1] tools_2.11.1 print(ces) yields: CnChipEffectSet: Name: Mcels Tags: QN,RMA,A+B Path: plmData/Mcels,QN,RMA,A+B/GenomeWideSNP_6 Platform: Affymetrix Chip type: GenomeWideSNP_6,Full,monocell Number of arrays: 4 Names: GM6, GM7, GM8, GM9 Time period: 2010-06-04 16:10:31 -- 2010-06-04 16:10:36 Total file size: 107.80MB RAM: 0.01MB Parameters: (probeModel: chr pm, mergeStrands: logi TRUE, combineAlleles: logi TRUE) -- 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/
