For Affymetrix, three types of files are currently supported: Affymetrix .CHP files, Affymetrix NetAffx annotation files and tab-delimited pivot or metrics files. Affymetrix .CEL files are currently not supported. However, the Bioconductor R package 'affy' allows you to preprocess the .CEL files and export a txt file containing a table of estimated gene-level expression values in three lines of code:
library(affy) # loading Bioconductor library 'affy' data=ReadAffy() # probe-level data import eset=rma(data) # probe-level data pre-processing using 'rma' write.exprs(eset,file="evals.txt") # writing gene expression levels to 'evals-txt'The exported txt file (evals.txt) can be imported into the workbench using the Generic expression data table format importer (Generic expression and annotation data file formats; you can just 'drag-and-drop' it in). In R, you should have all the CEL files you wish to process in your working directory and the file 'evals.txt' will be written to that directory.