Dear all, I am having some unusual problems with lumi under R 2.5. I've managed to read in a 30 sample experiment, Mouse6V1 arrays, and perform QC on the experiment. Everything looks OK up to that point. Then lumiT (variance stabilizing transformation) fails. What am I doing wrong? Thanks, Anand See below: Attaching package: 'lumi' The following object(s) are masked from package:affy : plotDensity > x.lumi <- lumiR("numbers.csv") > lumi.Q <- lumiQ(x.lumi) > lumi.Q Class: LumiQC Data dimension: 46120 genes x 30 samples Summary of Samples: 288 - 1 B6 NT 289 - 2 B6 NT 290 - 3 B6 NT 291 - 4 WT NT 292 - 5 WT NT 293 - 6 WT NT 294 - 7 CC NT 295 - 8 CC NT 296 - 9 CC NT 297 - 10 B6 D1 298 - 11 B6 D1 mean 7.45400 7.434000 7.360000 7.353000 7.338000 7.311000 7.334000 7.326000 7.210000 7.19200 7.123000 standard deviation 0.57440 0.569500 0.532400 0.549900 0.525700 0.551200 0.575200 0.585200 0.617900 0.55320 0.606000 detection rate 0.01477 0.007415 0.007307 0.009952 0.006592 0.007676 0.006331 0.007589 0.008825 0.01216 0.008174 distance to center 57.72000 58.910000 68.160000 62.670000 66.300000 60.200000 53.160000 55.570000 54.790000 55.69000 46.090000 299 - 12 B6 D1 300 - 13 WT D1 301 - 14 WT D1 302 - 15 WT D1 303 - 16 CC D1 304 - 17 CC D1 305 - 18 CC D1 669 - 19 B6 D2 673 - 23 WT D2 677 - 27 CC D2 mean 7.20000 7.089000 7.05300 7.05900 6.98800 6.95300 6.95400 7.41000 7.33000 7.328000 standard deviation 0.61760 0.599000 0.58730 0.59530 0.61640 0.61890 0.60660 0.89090 0.86930 0.881600 detection rate 0.01171 0.005919 0.01284 0.01245 0.01013 0.00657 0.01403 0.01043 0.01099 0.007719 distance to center 46.22000 49.890000 50.79000 50.27000 44.65000 47.71000 50.98000 69.85000 47.32000 56.680000 670 - 20 B6 D2 674 - 24 WT D2 678 - 28 CC D2 671 - 21 B6 D2 675 - 25 WT D2 679 - 29 CC D2 672 - 22 B6 D2 676 - 26 WT D2 680 - 30 CC D2 mean 7.37100 7.211000 7.24700 7.3060 7.355000 7.233000 7.094000 7.1430 7.109000 standard deviation 0.90650 0.813900 0.88630 0.9156 0.975700 0.899000 0.947400 0.9036 0.907400 detection rate 0.01073 0.009779 0.01095 0.0049 0.005464 0.007892 0.006353 0.0134 0.008781 distance to center 59.81000 54.570000 46.45000 48.0300 64.180000 45.270000 61.600000 52.4900 47.810000 Note: the detection threshold is 0.99, "center" is the mean of all samples. No outliers detected based on distance-to-center threshold 108. Major Operation History: submitted finished command 1 2007-03-02 13:38:14 2007-03-02 13:39:36 lumiR("numbers.csv") 2 2007-03-02 13:49:35 2007-03-02 13:49:49 lumiQ(x.lumi = x.lumi) > lumi.T <- lumiT(x.lumi) 2007-03-02 13:50:27 , processing array 1 Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases > x.lumi Data Information: Illumina Inc. BeadStudio version 1.5.1.3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Normalization = none,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Array Content = Mouse-6_V1.xml,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Error Model = none,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, DateTime = 6/13/2006 7:47 AM,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Local Settings = en-US,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Major Operation History: submitted finished command 1 2007-03-02 13:38:14 2007-03-02 13:39:36 lumiR("numbers.csv") Object Information: LumiBatch (storageMode: lockedEnvironment) assayData: 46120 features, 30 samples element names: beadNum, detection, exprs, se.exprs phenoData rowNames: 288 - 1 B6 NT, 289 - 2 B6 NT, ..., 680 - 30 CC D2 (30 total) varLabels and varMetadata: sampleID: The unique Illumina microarray Id label: The label of the sample featureData rowNames: 10181072_239_rc-S, 10181072_290_rc-S, ..., YFP_luxY-S (46120 total) varLabels and varMetadata: TargetID: The Illumina microarray identifier presentCount: The number of detectable measurements of the gene experimentData: use 'experimentData(object)' Annotation character(0)