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@@ -7,17 +7,12 @@
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# 1 Image patch extraction
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- Adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*, *config_testing.txt*, *config_normal.txt* and *config_tumor.txt*.
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- Run the commands listed in the following subsections to launch Son of Grid Engine (SGE) jobs to extract, group patches in HDF5 files and create a lookup table for every HDF5 file.
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-## 1.1 With color normalization
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-- qsub split_main.sh ./config_testing_cn_true.txt
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-- qsub split_main.sh ./config_normal_cn_true.txt
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-- qsub split_main.sh ./config_tumor_cn_true.txt
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-
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-## 1.2 Without color normalization
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+## 1.2 Extract and group
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- qsub split_main.sh ./config_testing.txt
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- qsub split_main.sh ./config_normal.txt
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- qsub split_main.sh ./config_tumor.txt
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-## 1.3 Creating lookup tables
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+## 1.3 Creat lookup tables
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- bash create_lookup_grp.sh ./config_testing.txt
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- bash create_lookup_grp.sh ./config_normal.txt
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- bash create_lookup_grp.sh ./config_tumor.txt
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Mike Mikailov