Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi. On Wed, Sep 29, 2010 at 10:32 AM, Prithish Banerjee prithish.baner...@gmail.com wrote: Respected Dr Bengtsson, Thank you for the help. I have done what you have suggested and the following output is as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data chipType - MoEx-1_0-st-v1 cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) print(cdf) ptf - AffymetrixProbeTabFile$byChipType(MoEx-1_0-st-v1); print(ptf) csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) csB - process(bc, cdf=cdf, ptf=ptf, verbose=verbose) 20100928 22:40:59|Background correcting data set... 20100928 22:41:09| Computing probe affinities... 20100928 22:41:09| Reading saved affinities: probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa... 20100928 22:41:10| Reading saved affinities: probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...done 20100928 22:41:10| RAM: 50.00MB 20100928 22:41:10| Computing probe affinities...done 20100928 22:41:10| Background correcting data set... 20100928 22:41:16| Already background corrected for optical effects 20100928 22:41:16| Background correcting data set...done 20100928 22:41:16| Estimating specific binding parameters... 20100928 22:41:16| Extracting PM indices... 20100928 22:41:16| Reading cell indices from CDF file... 20100928 22:41:16| Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf 20100928 22:41:16| Units: NULL 20100928 22:41:16| lapplyInChunks()... 20100928 22:41:16| Number of elements per chunk: 1e+05 20100928 22:41:16| Chunk #1 of 13... 20100928 22:41:16| Elements: int [1:10] 1 2 3 4 5 6 7 8 9 10 ... 20100928 22:41:16| Querying CDF file... 20100928 22:41:20| Querying CDF file...done 20100928 22:41:21| Restructuring... 20100928 22:41:21| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058626 110 6907341 368.9 17756025 948.3 Vcells 14800385 113 55506200 423.5 106800686 814.9 20100928 22:41:21| Chunk #1 of 13...done 20100928 22:41:21| Chunk #2 of 13... 20100928 22:41:21| Elements: int [1:10] 11 12 13 14 15 16 17 18 19 100010 ... 20100928 22:41:21| Querying CDF file... 20100928 22:41:25| Querying CDF file...done 20100928 22:41:26| Restructuring... 20100928 22:41:26| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058632 110.0 6907341 368.9 17756025 948.3 Vcells 14946933 114.1 44404960 338.8 106800686 814.9 20100928 22:41:26| Chunk #2 of 13...done 20100928 22:41:26| Chunk #3 of 13... 20100928 22:41:26| Elements: int [1:10] 21 22 23 24 25 26 27 28 29 200010 ... 20100928 22:41:26| Querying CDF file... 20100928 22:41:30| Querying CDF file...done 20100928 22:41:30| Restructuring... 20100928 22:41:30| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058634 110.0 6907341 368.9 17756025 948.3 Vcells 15101344 115.3 44404960 338.8 106800686 814.9 20100928 22:41:31| Chunk #3 of 13...done 20100928 22:41:31| Chunk #4 of 13... 20100928 22:41:31| Elements: int [1:10] 31 32 33 34 35 36 37 38 39 300010 ... 20100928 22:41:31| Querying CDF file... 20100928 22:41:35| Querying CDF file...done 20100928 22:41:35| Restructuring... 20100928 22:41:35| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058634 110.0 6907341 368.9 17756025 948.3 Vcells 15249056 116.4 44404960 338.8 106800686 814.9 20100928 22:41:36| Chunk #4 of 13...done 20100928 22:41:36| Chunk #5 of 13... 20100928 22:41:36| Elements: int [1:10] 41 42 43 44 45 46 47 48 49 400010 ... 20100928 22:41:36| Querying CDF file... 20100928 22:41:40| Querying CDF file...done 20100928 22:41:40| Restructuring... 20100928 22:41:40| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058635 110.0 6907341 368.9 17756025 948.3 Vcells 15397125 117.5 44404960 338.8 106800686 814.9 20100928 22:41:40| Chunk #5 of 13...done 20100928 22:41:40| Chunk #6 of 13... 20100928 22:41:40| Elements: int [1:10] 51 52 53 54 55
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Respected Dr Bengtsson, My codes and outputs are as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data chipType - MoEx-1_0-st-v1 cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf Filesize: 30.53MB Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 17831 Cells per unit: 367.54 Number of QC units: 1 csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) AffymetrixCelSet: Name: Exon Data Tags: Path: rawData/Exon Data/MoEx-1_0-st-v1 Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Number of arrays: 7 Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15 P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1) Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54 Total file size: 440.55MB RAM: 0.01MB cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) GcRmaBackgroundCorrection: Data set: Exon Data Input tags: User tags: * Asterisk ('*') tags: GRBC Output tags: GRBC Number of files: 7 (440.55MB) Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm, indicesNegativeControl: NULL, affinities: NULL, type: chr affinities, opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL) Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1 Is done: FALSE RAM: 0.00MB csB - process(bc, verbose=verbose) 20100927 16:31:40|Background correcting data set... 20100927 16:31:40| Computing probe affinities... 20100927 16:31:40| Computing GCRMA probe affinities for 1257006 units... 20100927 16:31:40| Identify PMs and MMs among the CDF cell indices... logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ... Mode FALSETRUENA's logical 334476 4931683 0 20100927 16:33:30|MMs are defined as non-PMs 20100927 16:33:30|Number of PMs: 4931683 20100927 16:33:30|Number of MMs: 334476 20100927 16:33:30| Identify PMs and MMs among the CDF cell indices...done 20100927 16:33:30| Reading probe-sequence data... 20100927 16:33:30|Retrieving probe-sequence data... 20100927 16:33:30| Chip type (full): MoEx-1_0-st-v1 20100927 16:33:30| Locating probe-tab file... 20100927 16:33:30| Chip type: MoEx-1_0-st-v1 Error in list(`process(bc, verbose = verbose)` = environment, `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment, : [2010-09-27 16:33:30] Exception: Found probe-tab file only by means of deprectated (v1) search rules: at throw(Exception(...)) at throw.default(Found probe-tab file only by means of deprectated (v1 at throw(Found probe-tab file only by means of deprectated (v1) search at method(static, ...) at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...) at method(static, ...) at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = at getProbeSequenceData(this, safe = safe, verbose = verbose) at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/ at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1, at do.call(bgAdjustGcrma, args = args) at process.GcRmaBackgroundCorrection( 20100927 16:33:30| Locating probe-tab file...done 20100927 16:33:30|Retrieving probe-sequence data...done 20100927 16:33:30| Reading probe-sequence data...done 20100927 16:33:30| Computing GCRMA probe affinities for 1257006 units...done 20100927 16:33:30| Computing probe affinities...done 20100927 16:33:30|Background correcting data set...done traceback() 17: throw.Exception(Exception(...)) 16: throw(Exception(...)) 15: throw.default(Found probe-tab file only by means of deprectated (v1) search rules: , pathname) 14: throw(Found probe-tab file only by means of deprectated (v1) search rules: , pathname) 13: method(static, ...) 12: AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...) 11: method(static, ...) 10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = less(verbose, 100)) 9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = verbose) 8: getProbeSequenceData(this, safe = safe, verbose = verbose) 7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., verbose = less(verbose)) 6: computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose)) 5:
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi, sorry, my mistake. I missed that you already did this. You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file. You can download it from Affymetrix and you'll find a link to their support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1 . Download it (something like MoEx-1_0-st-v1 Probe Sequences, tabular format (130 MB, 3/19/08)) and place it in annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is correct by trying the following: library(aroma.affymetrix); ptf - AffymetrixProbeTabFile$byChipType(MoEx-1_0-st-v1); ptf AffymetrixProbeTabFile: Name: MoEx-1_0-st-v1 Tags: Full name: MoEx-1_0-st-v1 Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab File size: 460.47 MB (482839635 bytes) RAM: 0.01 MB Number of data rows: NA Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness', 'category' Number of text lines: NA AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1.cdf Filesize: 274.30MB Chip type: MoEx-1_0-st-v1 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 1257006 Cells per unit: 5.21 Number of QC units: 0 If you get that to work, then your script should work. Let me now if this solved your problem. /Henrik On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee prithish.baner...@gmail.com wrote: Respected Dr Bengtsson, My codes and outputs are as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data chipType - MoEx-1_0-st-v1 cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf Filesize: 30.53MB Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 17831 Cells per unit: 367.54 Number of QC units: 1 csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) AffymetrixCelSet: Name: Exon Data Tags: Path: rawData/Exon Data/MoEx-1_0-st-v1 Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Number of arrays: 7 Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15 P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1) Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54 Total file size: 440.55MB RAM: 0.01MB cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) GcRmaBackgroundCorrection: Data set: Exon Data Input tags: User tags: * Asterisk ('*') tags: GRBC Output tags: GRBC Number of files: 7 (440.55MB) Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm, indicesNegativeControl: NULL, affinities: NULL, type: chr affinities, opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL) Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1 Is done: FALSE RAM: 0.00MB csB - process(bc, verbose=verbose) 20100927 16:31:40|Background correcting data set... 20100927 16:31:40| Computing probe affinities... 20100927 16:31:40| Computing GCRMA probe affinities for 1257006 units... 20100927 16:31:40| Identify PMs and MMs among the CDF cell indices... logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ... Mode FALSE TRUE NA's logical 334476 4931683 0 20100927 16:33:30| MMs are defined as non-PMs 20100927 16:33:30| Number of PMs: 4931683 20100927 16:33:30| Number of MMs: 334476 20100927 16:33:30| Identify PMs and MMs among the CDF cell indices...done 20100927 16:33:30| Reading probe-sequence data... 20100927 16:33:30| Retrieving probe-sequence data... 20100927 16:33:30| Chip type (full): MoEx-1_0-st-v1 20100927 16:33:30| Locating probe-tab file... 20100927 16:33:30| Chip type: MoEx-1_0-st-v1 Error in list(`process(bc, verbose = verbose)` = environment, `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment, : [2010-09-27 16:33:30] Exception: Found probe-tab file only by means of deprectated (v1) search rules: at throw(Exception(...)) at throw.default(Found probe-tab file only by means of deprectated (v1 at throw(Found probe-tab file only by means of deprectated (v1) search at method(static, ...) at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...) at method(static, ...) at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = at getProbeSequenceData(this, safe = safe, verbose = verbose) at
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi, first of all, for this chip type you need to specify: bc - GcRmaBackgroundCorrection(csR, type=affinities); Moreover, you cannot use the custom CDF in the GcRmaBackgroundCorrection step, and have to do the follow workaround illustrated in the below example: library(aroma.affymetrix); verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Affymetrix-Tissues; chipType - MoEx-1_0-st-v1; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Setup data set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cdf - AffymetrixCdfFile$byChipType(chipType, tags=coreR1,A20080718,MR); print(cdf); csR - AffymetrixCelSet$byName(dataSet, chipType=chipType); print(csR); # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # gcRMA-style background correction # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Currently, you must use the standard CDF file. cdf - getCdf(csR); cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)); setCdf(csR, cdfS); bc - GcRmaBackgroundCorrection(csR, type=affinities); print(bc); csB - process(bc, verbose=verbose); print(csB); # Now, use the custom CDF in what follows setCdf(csB, cdf); print(csB); Yes, those last steps are rather confusing - we're working on updating the code so you don't have to do that yourself. FYI, the above solution/workaround was resolved in thread 'GCRMA normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf. http://goo.gl/cniq. Hope this helps /Henrik On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee prithish.baner...@gmail.com wrote: Hi All, I am trying to normalize a mouse exon array dataset using GCRMA normalization technique. I have exactly followed all the necessary steps for storing the dataset and the cdf file. the code and the output I am using are as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data [the path in the working directory is rawData/Exon Data/MoEx-1_0-st-v1/*.CEL files] chipType - MoEx-1_0-st-v1 [the path in the working directory is annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf] cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) [converted to binary using convertCdf command] print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf Filesize: 30.53MB Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 17831 Cells per unit: 367.54 Number of QC units: 1 csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) AffymetrixCelSet: Name: Exon Data Tags: Path: rawData/Exon Data/MoEx-1_0-st-v1 Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Number of arrays: 7 Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15 P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1) Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54 Total file size: 440.55MB RAM: 0.01MB cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) GcRmaBackgroundCorrection: Data set: Exon Data Input tags: User tags: * Asterisk ('*') tags: GRBC Output tags: GRBC Number of files: 7 (440.55MB) Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm, indicesNegativeControl: NULL, affinities: NULL, type: chr affinities, opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL) Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1 Is done: FALSE RAM: 0.00MB csB - process(bc, verbose=verbose) 20100923 13:24:12|Background correcting data set... 20100923 13:24:12| Computing probe affinities... 20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units... 20100923 13:24:12| Identify PMs and MMs among the CDF cell indices... logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ... Mode FALSE TRUE NA's logical 334476 4931683 0 20100923 13:25:57| MMs are defined as non-PMs 20100923 13:25:57| Number of PMs: 4931683 20100923 13:25:57| Number of MMs: 334476 20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done 20100923 13:25:57| Reading probe-sequence data... 20100923 13:25:57| Retrieving probe-sequence data... 20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1 20100923 13:25:57| Locating probe-tab file... 20100923 13:25:57| Chip type: MoEx-1_0-st-v1 Error in list(`process(bc, verbose = verbose)` = environment, `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment, : [2010-09-23
[aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi All, I am trying to normalize a mouse exon array dataset using GCRMA normalization technique. I have exactly followed all the necessary steps for storing the dataset and the cdf file. the code and the output I am using are as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data [the path in the working directory is rawData/Exon Data/MoEx-1_0-st-v1/*.CEL files] chipType - MoEx-1_0-st-v1 [the path in the working directory is annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf] cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) [converted to binary using convertCdf command] print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf Filesize: 30.53MB Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 17831 Cells per unit: 367.54 Number of QC units: 1 csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) AffymetrixCelSet: Name: Exon Data Tags: Path: rawData/Exon Data/MoEx-1_0-st-v1 Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Number of arrays: 7 Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15 P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1) Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54 Total file size: 440.55MB RAM: 0.01MB cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) GcRmaBackgroundCorrection: Data set: Exon Data Input tags: User tags: * Asterisk ('*') tags: GRBC Output tags: GRBC Number of files: 7 (440.55MB) Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm, indicesNegativeControl: NULL, affinities: NULL, type: chr affinities, opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL) Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1 Is done: FALSE RAM: 0.00MB csB - process(bc, verbose=verbose) 20100923 13:24:12|Background correcting data set... 20100923 13:24:12| Computing probe affinities... 20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units... 20100923 13:24:12| Identify PMs and MMs among the CDF cell indices... logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ... Mode FALSETRUENA's logical 334476 4931683 0 20100923 13:25:57|MMs are defined as non-PMs 20100923 13:25:57|Number of PMs: 4931683 20100923 13:25:57|Number of MMs: 334476 20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done 20100923 13:25:57| Reading probe-sequence data... 20100923 13:25:57|Retrieving probe-sequence data... 20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1 20100923 13:25:57| Locating probe-tab file... 20100923 13:25:57| Chip type: MoEx-1_0-st-v1 Error in list(`process(bc, verbose = verbose)` = environment, `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment, : [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of deprectated (v1) search rules: at throw(Exception(...)) at throw.default(Found probe-tab file only by means of deprectated (v1 at throw(Found probe-tab file only by means of deprectated (v1) search at method(static, ...) at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...) at method(static, ...) at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = at getProbeSequenceData(this, safe = safe, verbose = verbose) at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/ at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1, at do.call(bgAdjustGcrma, args = args) at process.GcRmaBackgroundCorrection( 20100923 13:25:57| Locating probe-tab file...done 20100923 13:25:57|Retrieving probe-sequence data...done 20100923 13:25:57| Reading probe-sequence data...done 20100923 13:25:57| Computing GCRMA probe affinities for 1257006 units...done 20100923 13:25:57| Computing probe affinities...done 20100923 13:25:57|Background correcting data set...done Could anyone please enlighten me with the type of the error? I will be highly obliged if anyone please help me with this problem. Thank you. Prithish Banerjee. -- 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
[aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi All, I am trying to normalize a mouse exon array dataset using GCRMA normalization technique. I have exactly followed all the necessary steps for storing the dataset and the cdf file. the code and the output I am using are as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data [the path in the working directory is rawData/Exon Data/MoEx-1_0-st-v1/*.CEL files] chipType - MoEx-1_0-st-v1 [the path in the working directory is annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf] cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) [converted to binary using convertCdf command] print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf Filesize: 30.53MB Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 17831 Cells per unit: 367.54 Number of QC units: 1 csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) AffymetrixCelSet: Name: Exon Data Tags: Path: rawData/Exon Data/MoEx-1_0-st-v1 Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Number of arrays: 7 Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15 P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1) Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54 Total file size: 440.55MB RAM: 0.01MB cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) GcRmaBackgroundCorrection: Data set: Exon Data Input tags: User tags: * Asterisk ('*') tags: GRBC Output tags: GRBC Number of files: 7 (440.55MB) Platform: Affymetrix Chip type: MoEx-1_0-st-v1 Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm, indicesNegativeControl: NULL, affinities: NULL, type: chr affinities, opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL) Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1 Is done: FALSE RAM: 0.00MB csB - process(bc, verbose=verbose) 20100923 13:24:12|Background correcting data set... 20100923 13:24:12| Computing probe affinities... 20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units... 20100923 13:24:12| Identify PMs and MMs among the CDF cell indices... logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ... Mode FALSETRUENA's logical 334476 4931683 0 20100923 13:25:57|MMs are defined as non-PMs 20100923 13:25:57|Number of PMs: 4931683 20100923 13:25:57|Number of MMs: 334476 20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done 20100923 13:25:57| Reading probe-sequence data... 20100923 13:25:57|Retrieving probe-sequence data... 20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1 20100923 13:25:57| Locating probe-tab file... 20100923 13:25:57| Chip type: MoEx-1_0-st-v1 Error in list(`process(bc, verbose = verbose)` = environment, `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment, : [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of deprectated (v1) search rules: at throw(Exception(...)) at throw.default(Found probe-tab file only by means of deprectated (v1 at throw(Found probe-tab file only by means of deprectated (v1) search at method(static, ...) at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...) at method(static, ...) at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = at getProbeSequenceData(this, safe = safe, verbose = verbose) at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/ at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1, at do.call(bgAdjustGcrma, args = args) at process.GcRmaBackgroundCorrection( 20100923 13:25:57| Locating probe-tab file...done 20100923 13:25:57|Retrieving probe-sequence data...done 20100923 13:25:57| Reading probe-sequence data...done 20100923 13:25:57| Computing GCRMA probe affinities for 1257006 units...done 20100923 13:25:57| Computing probe affinities...done 20100923 13:25:57|Background correcting data set...done Could anyone please enlighten me with the type of the error? I will be highly obliged if anyone please help me with this problem. Thank you. Prithish Banerjee. -- 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