Affymetrix GeneChip
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 probe-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 probe 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.
If multiple probes are present for the same gene, further processing may be required to merge them into a single gene-level expression.
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