Convert Expression Set into a Matrix or Data Frame

Question

[Shab86]

Hi all,

I have an expression set which contains the following:

ExpressionSet
## assayData: 15905 features, 276 samples
##   element names: exprs
## protocolData: none
## phenoData
##   sampleNames: MNC5 MNC6 ... P0892 (276 total)
##   varLabels: HIPO-ID PID ... IC50batch (114 total)
##   varMetadata: labelDescription
## featureData
##   featureNames: D_001_1 D_001_2 ... ENSG00000273488 (15905 total)
##   fvarLabels: name type id subtype
##   fvarMetadata: labelDescription

Now I know how to access various elements i.e, RNA seq or DNA methylation data but its complicated and being a new user it becomes a tad bit difficult to use for further analysis etc. To make it easier I would like to convert it in a matrix or a data frame which can contain all the relevant data. For example, rows would be patient ID and columns can be other features like drugs and their dosages or methylation probe results or RNA seq results etc.

Is it possible to do so? Any help would be highly appreciated.

Thanks,
Shabbeer

Answer 1

[informatics bot]

have you tried using the exprs() function:

exprs(ExpressionSet)

also, the function:

pData(ExpressionSet)

should give you the corresponding phenotypic data you are interested in.

[Shab86]

I know exprs gives the main data i.e, some survival data in this case, and pData or fData for phenotypic or other features. But what I want to know is whether there is a method I can combine all of them into one simple matrix or data frame? That would make analysis easier. So, is that possible?

[informatics bot]

can't you just paste the phenotype data onto the column names for each sample within the expression matrix?

using the paste() and colnames() functions