1. NUGO Expression File Creator (by Caroline Reiff) Many programs in GenePattern require as input an expression dataset in RES or GCT file format. In order to make such a file from your dataset: Use the program Nugo Expression File Creator. You will need: A zipped folder containing your.CEL files (make sure the zip file name contains no spaces!) A.CLM file (make sure the CLM file name contains no spaces!) (a tab delineated txt file with.CLM file extension which shows for each chip in your dataset the CEL file name with extension in the first column, the sample name in the second column and the treatment in the third column as shown below for a dataset containing 6 chips) As.CELsampleAhighFat Bs.CELsampleBhighFat Cs.CELsampleChighFat Ds.CELsampleDlowFat Es.CELsampleElowFat Fs.CELsampleFlowFat Optionally: A probe description file (a tab delineated txt file containing the probe ID in column1 and the probe description in column2 for all probe IDs on the chip)

2. NUGO Expression File Creator upload zipped Cel files, upload.clm file, create GCT or RES file (RES file can only be created if MAS5 normalisation is selected) all other settings can be left at default settings For more information see the helpfile

3. NUGO Expression File Creator click RUN wait for the result

4. NUGO Expression File Creator The result will appear after a few minutes download result