Hello. I'm trying to read some raw (.cel) files generated from Affymetrix U133 Plus 2.0 Array using Brainarray custom CDFs. The code that I'm using are:
install.packages("http://mbni.org/customcdf/23.0.0/entrezg.download/pd.hgu133plus2.hs.entrezg_23.0.0.tar.gz", repos = NULL, type = "source") library(pd.hgu133plus2.hs.entrezg) library(oligo) path = #.cel files path raw_data <- read.celfiles(path, pkgname = "pd.hgu133plus2.hs.entrezg") normalized_data = oligo::rma(raw_data, target = "core")
read.CEL files runs well:
Platform design info loaded. Reading in : C:/Users/moosa/Desktop/Microarray/Projects/array/test/E-GEOD-71423/raw_data/GSM1834030_EA1242_06.CEL Reading in : C:/Users/moosa/Desktop/Microarray/Projects/array/test/E-GEOD-71423/raw_data/GSM1834029_EA1242_05.CEL Reading in : C:/Users/moosa/Desktop/Microarray/Projects/array/test/E-GEOD-71423/raw_data/GSM1834028_EA1242_04.CEL
When I'm not passing the argument
target = "core", the normalization process seems to be executed without a problem, but using the argument
target = "core" leads to the following error:
Background correcting... OK Normalizing... OK Available tables: featureSet1, mmfeature, mps1mm, mps1pm, pmfeature, table_info Error in getMPSInfo(get(annotation(object)), substr(target, 4, 4), "fid", : Table mpsepm does not exist.
thank you for your time. regards.