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$byChipType(chipType = chipType, verbose = les > at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = > at getProbeSequenceData(this, safe = safe, verbose = verbose) > at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver > at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos > at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/ > at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", > at do.call("bgAdjustGcrma", args = args) > at process.GcRmaBackgroundCorrection( > 20100927 16:33:30| Locating probe-tab file...done > 20100927 16:33:30| Retrieving probe-sequence data...done > 20100927 16:33:30| Reading probe-sequence data...done > 20100927 16:33:30| Computing GCRMA probe affinities for 1257006 > units...done > 20100927 16:33:30| Computing probe affinities...done > 20100927 16:33:30|Background correcting data set...done >> traceback() > 17: throw.Exception(Exception(...)) > 16: throw(Exception(...)) > 15: throw.default("Found probe-tab file only by means of deprectated (v1) > search rules: ", > pathname) > 14: throw("Found probe-tab file only by means of deprectated (v1) search > rules: ", > pathname) > 13: method(static, ...) > 12: AffymetrixProbeTabFile$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: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon > Data,GRBC/MoEx-1_0-st-v1", > verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, > typesToUpdate = "pm", indicesNegativeControl = NULL, affinities = > NULL, > type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE, > gsbParameters = NULL, .deprecated = FALSE) > 4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1", > verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL, > typesToUpdate = "pm", indicesNegativeControl = NULL, affinities = > NULL, > type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE, > gsbParameters = NULL, .deprecated = FALSE) > 3: do.call("bgAdjustGcrma", args = args) > 2: process.GcRmaBackgroundCorrection(bc, verbose = verbose) > 1: process(bc, verbose = verbose) >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-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_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0 > [4] R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1 > [7] matrixStats_0.2.1 R.rsp_0.4.0 R.filesets_0.9.0 > [10] digest_0.4.2 R.cache_0.3.0 R.utils_1.5.2 > [13] R.oo_1.7.4 R.methodsS3_1.2.1 > loaded via a namespace (and not attached): > [1] tools_2.11.1 > The working directory is desktop and the path for the cdf file and the raw > data is as follows: > /Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf > ( I have several other cdf files > like MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf > and MoEx-1_0-st-v1.cdf in the same directory.) > /Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/ > DK Litter D15 P1_(MoEx-1_0-st-v1).CEL > DK Litter D15 P2_(MoEx-1_0-st-v1).CEL > DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL > DK Litter D15 P3_(MoEx-1_0-st-v1).CEL > DK Litter D15 P6_(MoEx-1_0-st-v1).CEL > DK Litter D15 P14_(MoEx-1_0-st-v1).CEL > Moreover I am following the thread and implementing the code you suggested > there but it is not working with my dataset. Please help. > Thank you, > Prithish Banerjee, > Graduate Research Assistant, > Department of Statistics, > West Virginia University. > > On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <h...@aroma-project.org> > wrote: >> >> 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 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 >> > 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/ > > -- > 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/
