How can I reassign assayData slot of ExpressionSet?

Question

[wangshx]

When I use exprs function to reassign expression matrix to an ExpressionSet object, it does not work and an error occur. I want to remove the rows which cannot match any gene symbol.

A minimal code as follows can reproduce my error, someone who know how to do this correctly please help me, thanks.

> dataDirectory <- system.file("extdata", package="Biobase")
> exprsFile <- file.path(dataDirectory, "exprsData.txt")
> exprs <- as.matrix(read.table(exprsFile, header=TRUE, sep="\t",
+                               row.names=1,
+                               as.is=TRUE))
> minimalSet <- ExpressionSet(assayData=exprs)
> sdata <- matrix(0, nrow=400, ncol=26)
> exprs(minimalSet) <- sdata
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
> exprs(minimalSet) <- NULL  # here I want to assign NULL to arrayData and reassign sdata to it, but it fails
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘exprs<-’ for signature ‘"ExpressionSet", "NULL"’

Answer 1

[Kevin Blighe]

If you are filtering genes or samples from an ExpressionSet object, you do not have to access via the exprs() function. Just filter based on the name of the ExpressionSet object:

MyEset

ExpressionSet (storageMode: lockedEnvironment)
assayData: 194706 features, 22 samples

.

Select first 10 features and samples

MyEset[c(1:10),c(1:10)]

ExpressionSet (storageMode: lockedEnvironment)
assayData: 10 features, 10 samples

If you're trying to re-assign an entire 'new' expression matrix to your ExpressionSet object, then I do not see the utility in this. Just create another ExpressionSet object based on the new data matrix.

[wangshx]

Thank a lot. Your suggestion is practical.