Manual for MAI

Installation of MAI

You can download the source release here (the source will be locked until the paper acceptance).
(1) Unzip "MAI_V1.0.zip"
(2) Create a directory, move all the relevant files of MAI to that directory (Say MAI_DIR)
(3) Start MATLAB
(4) To set the path to MAI_DIR, click File->Set Path->Add Folder(MAI_DIR)->Save->Close
(5) Open "main_mai.m"
(6) line 9: Change working_dir to MAI_DIR

Synopsis of MAI

(1) We assume that your Affymetrix expression data are properly normalized by GCRMA (or RMA) (with R Bioconductor) and written in the csv files ("xxx.csv"). You can find an exmple csv file ("mydata.csv")
(2) Move all the relevant csv files to MAI_DIR
(3) The list of your csv files is stored in the input_file_mai file
("affy_data_integrate_test.txt", change the name at line 14 of "main_mai.m")
The format of input_file_mai:
xxx1.csv PLATFORM1
xxx2.csv PLATFORM2

An example:
GSE6489_HMVEC-L+HHV8.csv HG-U133_Plus_2
GSE7831_pDC+CpG-Influenza.csv Mouse430_2

(4) Run "main_mai.m"
(5) The normalized result will be written in the file ("result.txt", change the name at line 15 of "main_mai.m")