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/