Hi Henrik, I am testing the binary CDF files I created for various Gene ST arrays (re: discussion last Friday), but I run into problems. An error is occurring when reading the cell files. According to the change log this error has been reported before and should have been fixed by you (in version: 2.1.9 [2011-08-31]), so I don't know why this is happening. Could you please have a look?
This error occurs when trying to load mouse Gene ST v1.1 arrays; both in-house generated files as well as the ones downloaded from Affymetrix (http://www.affymetrix.com/support/downloads/demo_data/gene_1_1_st_ap_tissue_sample_data.zip). Idem for Affy-provided sample Gene ST v2.1 arrays. Remarkably, loading Gene ST v1.0 arrays goes fine... (I haven't tested any other array types yet). See below for code & output (first STv1.0 (=working); followed by STv1.1 (=failing)). Regards, Guido > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > # Gene ST v1.0 arrays (working) > chipType <- "MoGene-1_0-st-v1" > > cdf <- AffymetrixCdfFile$byChipType(chipType) > cdf AffymetrixCdfFile: Path: annotationData/chipTypes/MoGene-1_0-st-v1 Filename: MoGene-1_0-st-v1.cdf File size: 16.69 MB (17500618 bytes) Chip type: MoGene-1_0-st-v1 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 1050x1050 Number of cells: 1102500 Number of units: 28857 Cells per unit: 38.21 Number of QC units: 0 > cs <- AffymetrixCelSet$byName("guido", cdf=cdf); > cs AffymetrixCelSet: Name: guido Tags: Path: rawData/guido/MoGene-1_0-st-v1 Platform: Affymetrix Chip type: MoGene-1_0-st-v1 Number of arrays: 5 Names: A176_01_MCOLON_CD0_P1, A176_02_MCOLON_CD2_P2, A176_03_MCOLON_CD4_P3, A176_04_MCOLON_CD7_P4, A176_05_MCOLON_CD14_P5 [5] Time period: 2010-01-29 11:45:08 -- 2010-01-29 12:20:51 Total file size: 52.79MB RAM: 0.01MB > # Check CEL HEADER (using library AffxParser) > files <- list.files(pattern="[.](c|C)(e|E)(l|L)$") > if (length(files) > 0) { + header <- readCelHeader(files[1]) + print(header) + rm(header) + } $filename [1] "./A176_01_MCOLON_CD0_P1.CEL" $version [1] 4 $cols [1] 1050 $rows [1] 1050 $total [1] 1102500 $algorithm [1] "Percentile" $parameters [1] "Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:1;PoolHeightExtension:1;UseSubgrids:TRUE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;NumDATSubgrids:36" $chiptype [1] "MoGene-1_0-st-v1" $header [1] "Cols=1050\nRows=1050\nTotalX=1050\nTotalY=1050\nOffsetX=0\nOffsetY=0\nGridCornerUL=360 273\nGridCornerUR=7866 311\nGridCornerLR=7821 7775\nGridCornerLL=315 7737\nAxis-invertX=0\nAxisInvertY=0\nswapXY=0\nDatHeader=[1..20525] A176_01_mColon_cd0_p1:CLS=8341 RWS=8341 XIN=0 YIN=0 VE=30 2.0 01/29/10 11:45:08 50209050 M10 \024 \024 MoGene-1_0-st-v1.1sq \024 \024 \024 \024 \024 570 \024 25434.212891 \024 3.500000 \024 0.7000 \024 3\nAlgorithm=Percentile\nAlgorithmParameters=Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:1;PoolHeightExtension:1;UseSubgrids:TRUE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;NumDATSubgrids:36\n" $datheader [1] "[1..20525] A176_01_mColon_cd0_p1:CLS=8341 RWS=8341 XIN=0 YIN=0 VE=30 2.0 01/29/10 11:45:08 50209050 M10 \024 \024 MoGene-1_0-st-v1.1sq \024 \024 \024 \024 \024 570 \024 25434.212891 \024 3.500000 \024 0.7000 \024 3" $librarypackage [1] "" $cellmargin [1] 4 $noutliers [1] 12644 $nmasked [1] 0 > #Gene ST V1.1 arrays (fails) > chipType <- "MoGene-1_1-st-v1" > > cdf <- AffymetrixCdfFile$byChipType(chipType) > cdf AffymetrixCdfFile: Path: annotationData/chipTypes/MoGene-1_1-st-v1 Filename: MoGene-1_1-st-v1.cdf File size: 16.69 MB (17500604 bytes) Chip type: MoGene-1_1-st-v1 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 1190x990 Number of cells: 1178100 Number of units: 28857 Cells per unit: 40.83 Number of QC units: 0 > cs <- AffymetrixCelSet$byName("guido", cdf=cdf) > cs Error in if (hasTimestamp) { : argument is of length zero > # Check CEL HEADER > files <- list.files(pattern="[.](c|C)(e|E)(l|L)$") > if (length(files) > 0) { + header <- readCelHeader(files[1]) + print(header) + rm(header) + } $filename [1] "./G065_A05_02_TW188_344.CEL" $version [1] 1 $cols [1] 990 $rows [1] 1190 $total [1] 1178100 $algorithm [1] "HT Image Calibration Cell Generation" $parameters [1] "NumPixelsToUse:4;ImageCalibration:TRUE;FeatureExtraction:FALSE;IgnoreShiftRowOutliers:FALSE;FixedCellSize:TRUE;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;PercentileSpread:15.000000;StdMult:1.000000;ExtendPoolWidth:2;ExtendPoolHeight:2;OutlierLow:1.004000;OutlierHigh:1.500000;OutlierRatioLowPercentile:55;OutlierRatioHighPercentile:75;CellMargin:2;HalfCellRowsDivisor:5;HalfCellRowsRemainder:4;CellIntensityCalculationType:Percentile;Percentile:75;HighCutoff:2000;LowCutoff:4096;PairCutoff:0.000000;featureRows:174;featureColumns:201;featureWidth:5.000000;featureHeight:5.000000;GridULX:0.000000;GridULY:0.000000;GridURX:989.000000;GridURY:0.000000;GridLRX:989.000000;GridLRY:1189.000000;GridLLX:0.000000;GridLLY:1189.000000" $chiptype [1] "MoGene-1_1-st-v1" $header [1] "" $datheader [1] "" $librarypackage [1] "Expression" $cellmargin [1] 2 $noutliers [1] 0 $nmasked [1] 0 > > sessionInfo() R Under development (unstable) (2012-11-21 r61136) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_2.7.0 affxparser_1.31.1 aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.29.0 [6] aroma.core_2.7.1 matrixStats_0.6.2 R.rsp_0.8.2 R.devices_2.1.3 R.cache_0.6.5 [11] R.filesets_1.6.0 digest_0.6.0 R.utils_1.18.0 R.oo_1.11.3 R.methodsS3_1.4.2 loaded via a namespace (and not attached): [1] PSCBS_0.30.0 > -- 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. 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