Hi Devon,

I am using "inSilicoMerging" and getting an error message:

Error in (function (classes, fdef, mtable)  :  unable to find an inherited method for function 'annotation' for signature '"character"'

I Use R version 3.1.0 ; Bioconductor version 2.14; on Mac OS X 10.7.5

My steps:

(1) # From ArrayExpress I download 2 raw zip files: E-GEOD-52763 (E-GEOD-52763.raw.1.zip) and E_GEOD-45006 (E-GEOD-45006.raw.1.zip)

# code
library(affy)
library(annaffy)
ReadCell = ReadAffy()
Norm.data = rma(ReadCell)
eset1<-Norm.data

# code
eset2<-Norm.dat

# code:
library(inSilicomerging
> esets=list(eset1,eset2)
> eset_FRMA = merge(esets)

INSILICOMERGING: Run with no additional merging technique...
Error in (function (classes, fdef, mtable): unable to find an inherited method for function 'annotation' for signature '"character"'

or any other gave me the same error message:

> eset_BMC = merge(esets, method="BMC")
> eset_NULL = merge(esets, method=NULL, norm="FRMA", features = "GENE");
> eset_12 = merge(esets, method=NULL, norm="ORIGINAL");