[BioC] methylumi problem with subsetting samples

Dario Greco dario.greco at helsinki.fi
Wed May 11 15:18:26 CEST 2011


dear friends,
I am analyzing a dataset of illumina human methylation 450k arrays. i have the output from beadstudio, but no QC file to import.
i successfully imported the TAB-delimited text file exported from beadstudio by 

> lmdat<-methylumiR("DAT.txt")
> lmdat

Object Information:
MethyLumiSet (storageMode: environment)
assayData: 485577 features, 108 samples 
  element names: Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Intensity, betas, methylated, pvals, unmethylated 
protocolData: none
phenoData
  sampleNames: 5684819001_R01C01, 5684819001_R01C02, ..., 5729917056_R06C02  (108 total)
  varLabels and varMetadata description:
    sampleID: sampleID
    label: label
featureData
  featureNames: cg00000029, cg00000108, ..., rs9839873  (485577 total)
  fvarLabels and fvarMetadata description:
    Index: NA
    TargetID: NA
    ...: ...
    DHS: NA
    (37 total)
experimentData: use 'experimentData(object)'
Annotation:  
Major Operation History:
            submitted            finished                                          command
1 2011-05-11 15:47:46 2011-05-11 16:05:34 methylumiR(filename = "DAT.txt")


i can successfully subset features by:

> lmdat[1:10,]

Object Information:
MethyLumiSet (storageMode: environment)
assayData: 10 features, 108 samples 
  element names: Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Intensity, betas, methylated, pvals, unmethylated 
protocolData: none
phenoData
  sampleNames: 5684819001_R01C01, 5684819001_R01C02, ..., 5729917056_R06C02  (108 total)
  varLabels and varMetadata description:
    sampleID: sampleID
    label: label
featureData
  featureNames: cg00000029, cg00000108, ..., cg00000622  (10 total)
  fvarLabels and fvarMetadata description:
    Index: NA
    TargetID: NA
    ...: ...
    DHS: NA
    (37 total)
experimentData: use 'experimentData(object)'
Annotation:  
Major Operation History:
            submitted            finished                                          command
1 2011-05-11 15:47:46 2011-05-11 16:05:34 methylumiR(filename = "DAT.txt")
2 2011-05-11 16:11:01 2011-05-11 16:11:03                          Subsetting 10 features.


but when i try to subset samples, i get the following error:

> lmdat[,1:10]
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "QCdata<-", for signature "MethyLumiSet", "NULL"

i am working with R 2.11 and BioC 2.7 on a 64 bit mac os x 10.6.

any help is very appreciated.
thank you,
dario



More information about the Bioconductor mailing list