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ejh243 / BrainFANS

Complex Disease Epigenomics Group's quality control and analysis pipelines for DNA methylation arrays, SNP arrays, BS-Seq, ATAC-Seq and ChIP-Seq
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[Enhancement suggestion]: Pfilter for probe removal #192

Closed eld211 closed 1 week ago

eld211 commented 2 months ago

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Enhancement suggestion

Add pfilter step before the normalisation step in the normalisation script

ejh243 commented 2 months ago

Decided to add filter in prior to normalisation.

ejh243 commented 2 months ago

Decided not to filter cross hybridising and SNP probes as these lists are changed from time to time and may therefore require further manipulation post hoc.

Instead we will

  1. maintain a folder of these
  2. print a statement post normalisation to remind analyst that this needs to be done.