[BioC] problems with lumi

Fri Mar 2 21:05:54 CET 2007

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)