[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
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