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A Gene Pattern Question
Hi, I was referred here but not sure if this is the right place to ask. Any comments will be appreciated.
I am planning to run a Gene Pattern Module "CopyNumberInferencePipeline" on 240 tumor .CEL files, and roughly equivalent number of normal .CEL files. Since the module documentation specifically stated that the max number of CEL to be processed is 200, my strategy is to run the samples in batches. However, the noise reduction step relies on normal samples. For that reason, it will be the best to run all samples all together, which is beyond the max number specified. Any advice? If there is someone I can talk to regarding this, please point out.