I ran the following code to create and filter my "data" object:

data <- squareCounts(input, hg19.param, width=bin.size, filter=1)

keep <- aveLogCPM(asDGEList(data)) > 0

data <- data[keep,]

When I tried normalizing the filtered data using the following command I get the error below

data <- normOffsets(data, type="loess", se.out=TRUE)

Error in loessFit (log (mat [, x] + cont.cor.scaled [x]), ab, …) : unused argument (type = “loess” )

I tried running it on the initial data object and get the same error. Any ideas about how I can troubleshoot this error?

Pretty much as Lori said. The user's guide is (slightly) out of date, and I haven't had the opportunity to regenerate it, mostly because I no longer have access to the underlying files that are required for its generation.

In the meantime, the solution is to not use type="loess" when calling normOffsets(), as this function will always do a loess fit. (Conversely, normFactors() will always perform scaling normalization.) I separated the two modes of operation into different functions to avoid confusion, but must have missed an argument update.