I must start by saying that I'm just beginning to program using R. I'm unable to create expressionset of my data. When I try to put assaydata and phenodata together to make expressionset, I get an error:
Error in validObject(.Object) : " invalid class ""ExpressionSet"" object: sampleNames differ between assayData and phenoData"
Please take a look at the sample data, the phenodata table I made and R-program. I guess that the phenodata should be modified to get this working.
Please let me know how to solve this and alter phenodata.
AssayData
0h-1 0h-2 6h-1 6h-2 12h-1 12h-2 24h-1 24h-2 48h-1 48h-2 72h-1 72h-2 96h-1 96h-2
171407 4.021342514 4.021342514 6.847201005 6.847201005 3.189312274 3.189312274 3.322687671 3.322687671 4.929574559 4.929574559 4.040127938 4.040127938 3.181587044 3.181587044
171415 267.8091012 267.8091012 358.8511895 358.8511895 266.4562608 266.4562608 210.259177 210.259177 243.1496956 243.1496956 248.2780935 248.2780935 235.7079055 235.7079055
171426 13.3620332 13.3620332 5.581083074 5.581083074 12.5236932 12.5236932 8.433621131 8.433621131 13.07390505 13.07390505 12.94673202 12.94673202 23.43214156 23.43214156
171453 37.65310777 37.65310777 27.88942772 27.88942772 54.7409581 54.7409581 78.86045287 78.86045287 63.61655487 63.61655487 67.31327606 67.31327606 62.35426899 62.35426899
PhenoData
condition time rep
0h-1 Control 0 1
0h-2 Control 0 2
6h-1 treatment 6 1
6h-2 treatment 6 2
12h-1 treatment 12 1
12h-2 treatment 12 2
24h-1 treatment 24 1
24h-2 treatment 24 2
48h-1 treatment 48 1
48h-2 treatment 48 2
72h-1 treatment 72 1
72h-2 treatment 72 2
96h-1 treatment 96 1
96h-2 treatment 96 2
My Code:
library(""Biobase"")
library(""betr"")
exprs <- as.matrix(read.table(""Timecourse-Assaydata.txt"", header=TRUE, sep=""\t"", row.names=1, as.is=TRUE))
pData <- read.table(""Timecourse-Phenodata.txt"", row.names=1, header=TRUE, sep=""\t"")
metadata <- data.frame(labelDescription = c(""Hour of treatment"", ""Treatment time"", ""number of replicates""), row.names = c(""condition"", ""time"", ""rep""))
phenoData <- new(""AnnotatedDataFrame"", data = pData, varMetadata = metadata)
exprspop <- new(""ExpressionSet"", exprs = exprs, phenoData = phenoData)
Error in validObject(.Object) : " invalid class ""ExpressionSet"" object: sampleNames differ between assayData and phenoData"
Answer
The correct place for this question is on the Bioconductor support site. It's better to provide a reproducible example that captures the essence of the problem; creating the reproducible example often helps to identify the reason for the problem.
library(Biobase)
exprs <- matrix(0, nrow=5, ncol=3,
dimnames=list(letters[1:5], LETTERS[1:3]))
pData <- data.frame(id=c("foo", "bar", "baz"),
row.names=c("x", "y", "z"))
phenoData <- AnnotatedDataFrame(data=pData)
leading to
> ExpressionSet(exprs, phenoData=phenoData)
Error in validObject(.Object) :
invalid class "ExpressionSet" object: sampleNames differ between assayData and
phenoData
The problem is that the colname of exprs (i.e., the names of the samples in the experiment) differ frrom the row.names of pData (i.e., the description of the samples)
> row.names(pData)
[1] "x" "y" "z"
> colnames(exprs)
[1] "A" "B" "C"
and the solution is to make them the same
> colnames(exprs) <- row.names(pData)
> eset <- ExpressionSet(exprs, phenoData=phenoData)
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 5 features, 3 samples
element names: exprs
protocolData: none
phenoData
sampleNames: x y z
varLabels: id
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
Additional elements can be added to an existing ExpressionSet using assayDataReplace(), e.g.,
> assayDataElement(eset, "foo") <- sqrt(exprs)
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 5 features, 3 samples
element names: exprs, foo
protocolData: none
phenoData
sampleNames: x y z
varLabels: id
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
or from the start
> env = new.env()
> env$exprs = exprs
> env$sqrt = sqrt(exprs)
> lockEnvironment(env)
> ExpressionSet(env, pData=pData)
ExpressionSet (storageMode: environment)
assayData: 5 features, 3 samples
element names: exprs, sqrt
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation: