Question

I wanted to convert my dataframe of “array data” into an expressionSet. I followed this link and managed to get the same ( Expressionset – phenodata ) .

So i here get my expressionSet

> test
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1000 features, 733 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: X8261 X8164 ... X7727 (733 total)
  varLabels: Batch gender
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:

But now i would like to load/use this object/data inorder to use this for a particular R package “PVCA” (http://www.bioconductor.org/packages/2.12/bioc/vignettes/pvca/inst/doc/pvca.pdf) , so I do this:

> data(test)
Warning message:
In data(test) : data set âtestâ not found

I get this warning “data not found”. Can anyone help me know why do I get this? And what can I do to load my data and overcome this ?

Thanks in advance..

Answer 1

data is a function that returns a data set that the author of a package has included in the package. If your goal is to save the ExpressionSet across R sessions (this would not be necessary to use PVCA, just library(PVCA) in the same session in which you create the ExpressionSet) then use

save(test, file="test.Rda")

in one session and

load("test.Rda")

in another.