[aroma.affymetrix] Custom Canine SNP (DogSty06m520431); problem with chr24-39
Hi there, I hope you can help me with my problem since I have followed kind help with a similar problem on the google aroma.affymetrix formus, yet without the last bit of information I would need to succeed: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/96676bd38d64e884/e01329e5f44ba42b?lnk=gstq=building+ufl+file+for+DogSty06m520431#e01329e5f44ba42b We are processing the DogSty06m520431 chips and my Prof. wants me to generate CNV calculations for the corresponding samples. So far I could stick to the helpful guide on the aroma homepage for “Total Copy Number Analysis (GWS5 GWS6)”. Yet I am now faced with 2 problems of which I hope you could give me a hand. First one is that when executing the command: process(ce, chromosomes=c(38), verbose=verbose) for chromosomes 24 the analyses aborts with following prompting for e.g. chr25: process(ce, chromosomes=c(25), verbose=verbose) 20100823 13:05:15|Generating ChromosomeExplorer report... 20100823 13:05:15| Setting up ChromosomeExplorer report files... 20100823 13:05:15| Copying template files... 20100823 13:05:15| Source path: C:/Programme/R/R-2.11.1/library/ aroma.core/reports/includes 20100823 13:05:15| Destination path: reports/includes 20100823 13:05:23| Copying template files...done 20100823 13:05:23| Setting up ChromosomeExplorer report files...done 20100823 13:05:23| Explorer output version: 3 20100823 13:05:23| Compiling ChromosomeExplorer.onLoad.js.rsp... 20100823 13:05:23| Source: C:/Programme/R/R-2.11.1/library/aroma.core/ reports/templates/rsp/ChromosomeExplorer3/ ChromosomeExplorer.onLoad.js.rsp 20100823 13:05:23| Output path: reports/Weim/ACC,-XY,AVG,+300,A+B 20100823 13:05:23| Scanning directories for available chip types... 20100823 13:05:23| Detected chip types: DogSty06m520431 20100823 13:05:23| Scanning directories for available chip types...done 20100823 13:05:23| Scanning image files for available zooms... 20100823 13:05:24| Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64 20100823 13:05:24| Scanning image files for available zooms...done 20100823 13:05:24| Scanning directory for subdirectories... 20100823 13:05:24| Detected (or default) sets: cbs 20100823 13:05:24| Scanning directory for subdirectories...done 20100823 13:05:24| Compiling RSP... member data.class dimension objectSize 1chipTypes character 1 72 2chrLayers character 0 24 3 sampleLabels character 4264 4 sampleLayers character 0 24 5 samples character 4264 6 sets character 1 64 7zoomsnumeric 7 56 20100823 13:05:28| Sample names: [1] W24a_(DogSty06m520431) W469_(DogSty06m520431) W511_(DogSty06m520431) [4] W513_(DogSty06m520431) 20100823 13:05:28| Full sample names: [1] W24a_(DogSty06m520431) W469_(DogSty06m520431) W511_(DogSty06m520431) [4] W513_(DogSty06m520431) 20100823 13:05:28| Compiling RSP...done 20100823 13:05:29| Compiling ChromosomeExplorer.onLoad.js.rsp...done Loading required package: RColorBrewer Loading required package: Cairo 20100823 13:05:40| Building tuple of reference sets... 20100823 13:05:40| No reference available. 20100823 13:05:40| Calculating average copy-number signals... 20100823 13:05:40| Retrieving average cell signals across 4 arrays... CnChipEffectFile: Name: .average-intensities-median-mad Tags: f1b4541a56b9bb2404325d6053edc91e Full name: .average-intensities-median- mad,f1b4541a56b9bb2404325d6053edc91e Pathname: plmData/Weim,ACC,-XY,AVG,+300,A+B/ DogSty06m520431/.average-intensities-median- mad,f1b4541a56b9bb2404325d6053edc91e.CEL File size: 4.86 MB (5091526 bytes) RAM: 0.01 MB File format: v4 (binary; XDA) Platform: Affymetrix Chip type: DogSty06m520431,monocell Timestamp: 2010-08-19 11:56:52 Parameters: (probeModel: chr pm, mergeStrands: logi TRUE, combineAlleles: logi TRUE) 20100823 13:05:40| Retrieving average cell signals across 4 arrays...done 20100823 13:05:41| Calculating average copy-number signals...done 20100823 13:05:41| Building tuple of reference sets...done 20100823 13:05:41| Using reference tuple: CnChipEffectSetTuple: Name: Weim Tags: ACC,-XY,AVG,+300,A+B Chip types: DogSty06m520431 CnChipEffectSet: Name: Weim Tags: ACC,-XY,AVG,+300,A+B Path: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431 Platform: Affymetrix Chip type: DogSty06m520431,monocell Number of arrays: 4 Names: .average-intensities-median-mad, .average-intensities-median- mad, .average-intensities-median-mad, .average-intensities-median-mad Time period: 2010-08-19 11:56:52 -- 2010-08-19 11:56:52 Total file size: 19.42MB RAM: 0.01MB Parameters: (probeModel: chr pm, mergeStrands: logi TRUE, combineAlleles: logi TRUE) RAM: 0.00MB 20100823 13:05:41| Extract DataFileMatrix... 20100823 13:05:41| Array: 1 20100823 13:05:41| Test data sets:
Re: [aroma.affymetrix] Custom Canine SNP (DogSty06m520431); problem with chr24-39
Hi Denis, you refer to the thread 'Custom Canine SNP' started on July 18, 2008. In KD's message on August 14, 2008 you can see how he explicitly set argument genome=Canine when he sets up the GLAD model. From the verbose output I can see you are using CBS, but it is not clear how you set it up. Are you doing: cbs - CbsModel(ces, genome=Canine)? If not, do that. Then (for troubleshooting purposes only) try df - getGenomeData(cbs, verbose=verbose); print(df); This latter step will try to load the tab-delimited file containing the information about the number of bases per chromosomes. Since you specify Canine above, it will try to locate and read the file: annotationData/genomes/Canine/Canine,chromosomes.txt or any with additional tags, e.g. annotationData/genomes/Canine/Canine,chromosomes,UGP,HB20100822.txt It needs to contain (at least) the two columns chromosome and nbrOfBases. I don't have the exact numbers for the Canine genome, but see the attached file for an example. Feel free to forward the data to me, and I'll add this Canine annotation data so it's built in to the aroma framework. If you get the above working once, then process(ce) should work too. Hope this helps Henrik On Mon, Aug 23, 2010 at 4:28 AM, Denis amer.ak...@rub.de wrote: Hi there, I hope you can help me with my problem since I have followed kind help with a similar problem on the google aroma.affymetrix formus, yet without the last bit of information I would need to succeed: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/96676bd38d64e884/e01329e5f44ba42b?lnk=gstq=building+ufl+file+for+DogSty06m520431#e01329e5f44ba42b We are processing the DogSty06m520431 chips and my Prof. wants me to generate CNV calculations for the corresponding samples. So far I could stick to the helpful guide on the aroma homepage for “Total Copy Number Analysis (GWS5 GWS6)”. Yet I am now faced with 2 problems of which I hope you could give me a hand. First one is that when executing the command: process(ce, chromosomes=c(38), verbose=verbose) for chromosomes 24 the analyses aborts with following prompting for e.g. chr25: process(ce, chromosomes=c(25), verbose=verbose) 20100823 13:05:15|Generating ChromosomeExplorer report... 20100823 13:05:15| Setting up ChromosomeExplorer report files... 20100823 13:05:15| Copying template files... 20100823 13:05:15| Source path: C:/Programme/R/R-2.11.1/library/ aroma.core/reports/includes 20100823 13:05:15| Destination path: reports/includes 20100823 13:05:23| Copying template files...done 20100823 13:05:23| Setting up ChromosomeExplorer report files...done 20100823 13:05:23| Explorer output version: 3 20100823 13:05:23| Compiling ChromosomeExplorer.onLoad.js.rsp... 20100823 13:05:23| Source: C:/Programme/R/R-2.11.1/library/aroma.core/ reports/templates/rsp/ChromosomeExplorer3/ ChromosomeExplorer.onLoad.js.rsp 20100823 13:05:23| Output path: reports/Weim/ACC,-XY,AVG,+300,A+B 20100823 13:05:23| Scanning directories for available chip types... 20100823 13:05:23| Detected chip types: DogSty06m520431 20100823 13:05:23| Scanning directories for available chip types...done 20100823 13:05:23| Scanning image files for available zooms... 20100823 13:05:24| Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64 20100823 13:05:24| Scanning image files for available zooms...done 20100823 13:05:24| Scanning directory for subdirectories... 20100823 13:05:24| Detected (or default) sets: cbs 20100823 13:05:24| Scanning directory for subdirectories...done 20100823 13:05:24| Compiling RSP... member data.class dimension objectSize 1 chipTypes character 1 72 2 chrLayers character 0 24 3 sampleLabels character 4 264 4 sampleLayers character 0 24 5 samples character 4 264 6 sets character 1 64 7 zooms numeric 7 56 20100823 13:05:28| Sample names: [1] W24a_(DogSty06m520431) W469_(DogSty06m520431) W511_(DogSty06m520431) [4] W513_(DogSty06m520431) 20100823 13:05:28| Full sample names: [1] W24a_(DogSty06m520431) W469_(DogSty06m520431) W511_(DogSty06m520431) [4] W513_(DogSty06m520431) 20100823 13:05:28| Compiling RSP...done 20100823 13:05:29| Compiling ChromosomeExplorer.onLoad.js.rsp...done Loading required package: RColorBrewer Loading required package: Cairo 20100823 13:05:40| Building tuple of reference sets... 20100823 13:05:40| No reference available. 20100823 13:05:40| Calculating average copy-number signals... 20100823 13:05:40| Retrieving average cell signals across 4 arrays... CnChipEffectFile: Name: .average-intensities-median-mad Tags: f1b4541a56b9bb2404325d6053edc91e Full name: .average-intensities-median- mad,f1b4541a56b9bb2404325d6053edc91e Pathname: plmData/Weim,ACC,-XY,AVG,+300,A+B/
