Hi Sharon,
This is how we do it. It is a bit complicated as you can see.
The assumption is that variable signalRaw contains a matrix
with raw intensities (one column per sample). Variable beadSD
contains a similar matrix but for bead sd's. I think that
bead sd's are required for LumiBatch to work properly.
library( lumi )
#############################################
# Fake feature information
featureIndices <- 1 : nrow( signalRaw )
featureNames <- paste( "f", featureIndices, sep = "" )
rownames( signalRaw ) <- rownames( beadSD ) <- featureNames
reporterInfo <- data.frame( featureNames )
names( reporterInfo ) <- "DummyID"
rownames( reporterInfo ) <- featureNames
varMetadata <- data.frame( labelDescription = "A dummy Illumina
feature identifier" )
rownames( varMetadata ) <- "DummyID"
featureData <- new( "AnnotatedDataFrame", data = reporterInfo,
varMetadata = varMetadata )
#############################################
# Fake sample information
sampleIndices <- 1 : ncol( signalRaw )
sampleNames <- paste( "sample", sampleIndices, sep = "" )
colnames( signalRaw ) <- colnames( beadSD ) <- sampleNames
pData <- data.frame( sampleNames )
names( pData ) <- "sampleID"
rownames( pData ) <- sampleNames
varMetadata <- data.frame( labelDescription = "A dummy sample ID"
)
rownames( varMetadata ) <- "sampleID"
phenoData <- new( "AnnotatedDataFrame", data = pData, varMetadata
= varMetadata )
#############################################
# Create the LumiBatch object
lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs =
beadSD,
featureData = featureData, phenoData = phenoData )
Best,
Michal Blazejczyk
> Hi,
> I have an Illumina array data in the matrix form. I would like
> to create a LumiBatch object leaving all the slots empty except
> the exprs slot. Is it possible to do that? If so, how?
> I would greatly appreciate any help from you.
> Thanks in advance.
> Kind regards,
> Sharon
