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@@ -5,7 +5,7 @@
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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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+- Adjust configuration parameters in files *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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## 1.2 Extract and group
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- qsub split_main.sh ./config_testing.txt
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@@ -20,7 +20,8 @@
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The lookup tables are created only once and used at [Prediction](#2-prediction) stage for launching array job tasks. These tasks are run in parallel and scalable manner - if there are not enough resourcs for running all tasks then they are queued up automatically and started as resources become available. Each task processes only one group.
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# 2 Prediction
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-Run the below commands to launch SGE jobs to generate prediction matrices.
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+- Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*.
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+- Run the below commands to launch SGE jobs to generate prediction matrices.
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## 2.1 With color normalization
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- qsub process_main.sh ./config_testing_cn_true.txt
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- qsub process_main.sh ./config_normal_cn_true.txt
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Mike Mikailov