R Under development (unstable) (2024-02-17 r85935 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.affymetrix") Loading required package: R.utils Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help. Attaching package: 'R.oo' The following object is masked from 'package:R.methodsS3': throw The following objects are masked from 'package:methods': getClasses, getMethods The following objects are masked from 'package:base': attach, detach, load, save R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help. Attaching package: 'R.utils' The following object is masked from 'package:utils': timestamp The following objects are masked from 'package:base': cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings Loading required package: aroma.core Loading required package: R.filesets R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help. Attaching package: 'R.filesets' The following object is masked from 'package:R.utils': validate The following objects are masked from 'package:base': append, readLines Loading required package: R.devices R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help. aroma.core v3.3.0 (2022-11-15 18:30:13 UTC) successfully loaded. See ?aroma.core for help. Attaching package: 'aroma.core' The following objects are masked from 'package:base': .Machine, colMeans, colSums, library, require, write Loading required package: aroma.light aroma.light v3.32.0 (2023-10-24) successfully loaded. See ?aroma.light for help. Attaching package: 'aroma.light' The following objects are masked from 'package:aroma.affymetrix': averageQuantile, normalizeQuantile, plotDensity, plotMvsA, plotXYCurve The following objects are masked from 'package:aroma.core': callNaiveGenotypes, normalizeTumorBoost Loading required package: affxparser Attaching package: 'affxparser' The following object is masked from 'package:aroma.affymetrix': writeCdf The following object is masked from 'package:R.utils': findFiles The following object is masked _by_ package:aroma.affymetrix: writeCdf The following object is masked from package:R.utils: findFiles aroma.affymetrix v3.2.2 successfully loaded. See ?aroma.affymetrix for help. Attaching package: 'aroma.affymetrix' The following objects are masked _by_ 'package:aroma.light': averageQuantile, normalizeQuantile, plotDensity, plotMvsA, plotXYCurve The following object is masked from 'package:affxparser': writeCdf > > ## Empty CEL set > ds <- AffymetrixCelSet() > print(ds) AffymetrixCelSet: Name: NA Tags: Path: NA Platform: Affymetrix Chip type: NA Number of arrays: 0 Time period: NA Total file size: 0 B > > ## Extract non-existing subset on empty set > ds <- AffymetrixCelSet() > dsT <- extract(ds, "foo", onMissing="NA") > print(dsT) AffymetrixCelSet: Name: NA Tags: Path: NA Platform: Affymetrix Chip type: NA Number of arrays: 1 Names: NA [1] Time period: NA -- NA Total file size: 0 B > > ## CEL set with non-existing CEL file > files <- list(AffymetrixCelFile()) > ds <- AffymetrixCelSet(files) > print(ds) AffymetrixCelSet: Name: NA Tags: Path: NA Platform: Affymetrix Chip type: NA Number of arrays: 1 Names: NA [1] Time period: NA -- NA Total file size: 0 B > > > if (setupExampleData(aroma.affymetrix, mustWork=FALSE)) { + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # CDF file + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + cdf <- AffymetrixCdfFile$byChipType("HG-Focus") + print(cdf) + + # Unit names, types, ... + names <- getUnitNames(cdf) + str(names) + + units <- indexOf(cdf, names=names[42:40]) + stopifnot(all.equal(units, 42:40)) + + types <- getUnitTypes(cdf) + print(table(types)) + + data <- readUnits(cdf, units=1:10) + str(data) + + data <- readDataFrame(cdf, units=1:10) + str(data) + + md5 <- getChecksumFile(cdf) + print(md5) + + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # CEL set / CEL file + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + cels <- AffymetrixCelSet$byName("FusionSDK_HG-Focus", cdf=cdf) + print(cels) + + # A single file + cel <- cels[[1]] + print(cel) + + # File checksums + md5s <- getChecksumFileSet(cels) + print(md5s) + + # File checksums + md5 <- getChecksumFile(cel) + print(md5) + + # Average CEL file + celR <- getAverageFile(cels) + print(celR) + + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # AromaPlatformInterface + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + platform <- getAromaPlatform(cdf) + print(platform) + stopifnot(equals(getAromaPlatform(cels), platform)) + stopifnot(equals(getAromaPlatform(cel), platform)) + + # Unit names file + unf <- getUnitNamesFile(cdf) + print(unf) + stopifnot(equals(getUnitNamesFile(cels), unf)) + stopifnot(equals(getUnitNamesFile(cel), unf)) + } # if (require("AffymetrixDataTestFiles")) AffymetrixCdfFile: Path: annotationData/chipTypes/HG-Focus Filename: HG-Focus.CDF File size: 4.06 MiB (4261873 bytes) Chip type: HG-Focus File format: v4 (binary; XDA) Dimension: 448x448 Number of cells: 200704 Number of units: 8793 Cells per unit: 22.83 Number of QC units: 10 chr [1:8793] "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at" ... types 1 8793 List of 10 $ AFFX-BioB-5_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioB-5_at:List of 6 .. .. ..$ x : int [1:40] 216 216 217 217 218 218 219 219 220 220 ... .. .. ..$ y : int [1:40] 264 265 264 265 264 265 264 265 264 265 ... .. .. ..$ pbase : chr [1:40] "A" "T" "C" "G" ... .. .. ..$ tbase : chr [1:40] "T" "T" "G" "G" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-BioB-M_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioB-M_at:List of 6 .. .. ..$ x : int [1:40] 218 218 219 219 220 220 221 221 222 222 ... .. .. ..$ y : int [1:40] 266 267 266 267 266 267 266 267 266 267 ... .. .. ..$ pbase : chr [1:40] "C" "G" "T" "A" ... .. .. ..$ tbase : chr [1:40] "G" "G" "A" "A" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-BioB-3_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioB-3_at:List of 6 .. .. ..$ x : int [1:40] 220 220 221 221 222 222 223 223 224 224 ... .. .. ..$ y : int [1:40] 268 269 268 269 268 269 268 269 268 269 ... .. .. ..$ pbase : chr [1:40] "C" "G" "C" "G" ... .. .. ..$ tbase : chr [1:40] "G" "G" "G" "G" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-BioC-5_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioC-5_at:List of 6 .. .. ..$ x : int [1:40] 222 222 223 223 224 224 225 225 226 226 ... .. .. ..$ y : int [1:40] 270 271 270 271 270 271 270 271 270 271 ... .. .. ..$ pbase : chr [1:40] "G" "C" "C" "G" ... .. .. ..$ tbase : chr [1:40] "C" "C" "G" "G" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-BioC-3_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioC-3_at:List of 6 .. .. ..$ x : int [1:40] 224 224 225 225 226 226 227 227 228 228 ... .. .. ..$ y : int [1:40] 272 273 272 273 272 273 272 273 272 273 ... .. .. ..$ pbase : chr [1:40] "A" "T" "T" "A" ... .. .. ..$ tbase : chr [1:40] "T" "T" "A" "A" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-BioDn-5_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioDn-5_at:List of 6 .. .. ..$ x : int [1:40] 226 226 227 227 228 228 229 229 230 230 ... .. .. ..$ y : int [1:40] 274 275 274 275 274 275 274 275 274 275 ... .. .. ..$ pbase : chr [1:40] "G" "C" "A" "T" ... .. .. ..$ tbase : chr [1:40] "C" "C" "T" "T" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-BioDn-3_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-BioDn-3_at:List of 6 .. .. ..$ x : int [1:40] 228 228 229 229 230 230 231 231 232 232 ... .. .. ..$ y : int [1:40] 276 277 276 277 276 277 276 277 276 277 ... .. .. ..$ pbase : chr [1:40] "T" "A" "T" "A" ... .. .. ..$ tbase : chr [1:40] "A" "A" "A" "A" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-CreX-5_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-CreX-5_at:List of 6 .. .. ..$ x : int [1:40] 230 230 231 231 232 232 233 233 216 216 ... .. .. ..$ y : int [1:40] 278 279 278 279 278 279 278 279 280 281 ... .. .. ..$ pbase : chr [1:40] "T" "A" "C" "G" ... .. .. ..$ tbase : chr [1:40] "A" "A" "G" "G" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-CreX-3_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-CreX-3_at:List of 6 .. .. ..$ x : int [1:40] 232 232 233 233 216 216 217 217 218 218 ... .. .. ..$ y : int [1:40] 280 281 280 281 282 283 282 283 282 283 ... .. .. ..$ pbase : chr [1:40] "C" "G" "A" "T" ... .. .. ..$ tbase : chr [1:40] "G" "G" "T" "T" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-HUMISGF3A/M97935_5_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-HUMISGF3A/M97935_5_at:List of 6 .. .. ..$ x : int [1:40] 443 443 249 249 390 390 266 266 416 416 ... .. .. ..$ y : int [1:40] 331 332 123 124 335 336 285 286 331 332 ... .. .. ..$ pbase : chr [1:40] "C" "G" "G" "C" ... .. .. ..$ tbase : chr [1:40] "G" "G" "C" "C" ... .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 'data.frame': 400 obs. of 16 variables: $ unit : int 1 1 1 1 1 1 1 1 1 1 ... $ unitName : chr "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ unitNbrOfAtoms : int 20 20 20 20 20 20 20 20 20 20 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" ... $ groupDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ groupNbrOfAtoms: int 20 20 20 20 20 20 20 20 20 20 ... $ cell : int 118489 118937 118490 118938 118491 118939 118492 118940 118493 118941 ... $ x : int 216 216 217 217 218 218 219 219 220 220 ... $ y : int 264 265 264 265 264 265 264 265 264 265 ... $ pbase : chr "A" "T" "C" "G" ... $ tbase : chr "T" "T" "G" "G" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... ChecksumFile: Name: HG-Focus.CDF Tags: Full name: HG-Focus.CDF Pathname: annotationData/chipTypes/HG-Focus/HG-Focus.CDF.md5 File size: 32 B (32 bytes) Checksum on record: 307006493ef52faf137da0bd84c59ca8 AffymetrixCelSet: Name: HG-Focus Tags: Path: ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin Platform: Affymetrix Chip type: HG-Focus Number of arrays: 2 Names: HG-Focus-1-121502, HG-Focus-2-121502 [2] Time period: 2002-05-15 10:59:33 -- 2002-05-15 11:07:10 Total file size: 3.84 MiB AffymetrixCelFile: Name: HG-Focus-1-121502 Tags: Full name: HG-Focus-1-121502 Pathname: ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL File size: 1.92 MiB (2012775 bytes) File format: v1 (binary; CC) Platform: Affymetrix Chip type: HG-Focus Timestamp: 2002-05-15 11:07:10 ChecksumFileSet: Name: 2.Calvin Tags: Full name: 2.Calvin Number of files: 2 Names: HG-Focus-1-121502.CEL, HG-Focus-2-121502.CEL [2] Path (to the first file): ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin Total file size: 64 B (64 bytes) ChecksumFile: Name: HG-Focus-1-121502.CEL Tags: Full name: HG-Focus-1-121502.CEL Pathname: ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL.md5 File size: 32 B (32 bytes) Checksum on record: eb680c1b324e74b649e8b7fc643ee0c5 AffymetrixCelFile: Name: .average-intensities-median-mad Tags: b6c18433fdbd8c5edcea9dc2fa49c6aa Full name: .average-intensities-median-mad,b6c18433fdbd8c5edcea9dc2fa49c6aa Pathname: ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/.average-intensities-median-mad,b6c18433fdbd8c5edcea9dc2fa49c6aa.CEL File size: 1.91 MiB (2007713 bytes) File format: v4 (binary; XDA) Platform: Affymetrix Chip type: HG-Focus Timestamp: 2023-04-08 06:16:18 AffymetrixPlatform: Platform: Affymetrix AffymetrixCdfFile: Path: annotationData/chipTypes/HG-Focus Filename: HG-Focus.CDF File size: 4.06 MiB (4261873 bytes) Chip type: HG-Focus File format: v4 (binary; XDA) Dimension: 448x448 Number of cells: 200704 Number of units: 8793 Cells per unit: 22.83 Number of QC units: 10 Warning message: In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF", : Some of the fields were not read: expos > > proc.time() user system elapsed 1.87 0.23 4.20