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Hi all,
I must admit that I am quite new to both methylation data analysis and
R. I am currently analyzing IlluminaHumanMethylation450k array. Before
using BMIQ method I have used lumi package to perform a background
correction and created a MethyLumiM object. Is it possible to use
MethyLumiM object as input in BMIQ method? When I try to use it, I got
following error:
> BMIQ.AvgBeta_24=BMIQ(AvgBeta_24, nfit=100)
Error in BMIQ(AvgBeta_24, nfit = 100) :
argument "design.v" is missing, with no default
In addition: Warning message:
In is.na(beta.v) : is.na() applied to non-(list or vector) of type
'S4'
However if I use methylumi package to load my data which creates a
MethyLumiSet object, BMIQ is working fine with me. Please suggest me
if there is any alternative way to use MethyLumiM object as input for
BMIQ method.
Below I am attaching the description of both the objects.
Thanks for your help.
> AvgBeta_24
MethyLumiM (storageMode: lockedEnvironment)
assayData: 485577 features, 24 samples
element names: detection, exprs, methylated, unmethylated
protocolData: none
phenoData
sampleNames: BEA1_NGT BEA13_T2DM ... BEA24_Lean (24 total)
varLabels: sampleID label
varMetadata: labelDescription
featureData
featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total)
fvarLabels: Index TargetID ... POSITION (8 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> AvgBeta_methylumi
Object Information:
MethyLumiSet (storageMode: lockedEnvironment)
assayData: 485577 features, 24 samples
element names: betas, Intensity, methylated, pvals, unmethylated
protocolData: none
phenoData
sampleNames: BEA1_NGT BEA13_T2DM ... BEA24_Lean (24 total)
varLabels: sampleID label
varMetadata: labelDescription
featureData
featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total)
fvarLabels: Index TargetID ... ProbeID_B (6 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
Major Operation History:
submitted finished
1 2013-04-16 09:15:46 2013-04-16 09:17:03
command
1 methylumiR(filename = "Avg_Beta_values_24samples.txt", lib =
"IlluminaHumanMethylation450k.db")
Best regards,
Indranil.
-- output of sessionInfo():
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252
LC_MONETARY=Swedish_Sweden.1252
[4] LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] wateRmelon_1.0.0 ROC_1.36.0
IlluminaHumanMethylation450k.db_2.0.7
[4] org.Hs.eg.db_2.9.0 RSQLite_0.11.2
DBI_0.2-5
[7] AnnotationDbi_1.22.1 lumi_2.12.0
matrixStats_0.6.2
[10] limma_3.16.1 RPMM_1.10
cluster_1.14.4
[13] BiocInstaller_1.10.0 methylumi_2.6.1
ggplot2_0.9.3.1
[16] reshape2_1.2.2 scales_0.2.3
Biobase_2.20.0
[19] BiocGenerics_0.6.0
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(c("affy", "affyio", "annotate", "beanplot", "Biostrings", :
DESCRIPTION file of package 'colorspace' is missing or broken
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