I've been able to create a summarized experiment but I'm having some difficulty subsetting and expressing my data. For example, I have arranged my summarizedexperiment by gene with RNA-seq (seq) and methylation data (methyl) See example code:

seq <- data.frame("GAPDH" = c(1,5,NA, NA), "ACTB" = c(10,15, NA, NA))

methyl <- data.frame("GAPDH" = c(10,20,0,0), "ACTB" = c(0,0,50,100))

A = SummarizedExperiment(assays=list(seq,methyl))

what I'd like to be able to do next is to pull both the seq and methyl data for "GAPDH". 

I realize that this is probably simple but I've looked over the subsetting section and am still have some difficulty figuring it out. 

Typically in genomics, rows are features while columns are samples. So we would generally expect:

A <- SummarizedExperiment(assays=list(t(seq),t(methyl)))

... such that you can subset with:

subA <- A["GAPDH",]

... and then get the RNA-seq or methylation data with:

assay(subA, 1) # seq
assay(subA, 2) # methyl

You can also name the assays to make it easier for yourself when you're extracting the data, instead of having to remember that the first assay is RNA-seq and the second assay is methylation.