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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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Normalisation script Cell.type vs Cell_Type[Bug]: #135

Closed AnthonyKl98 closed 5 months ago

AnthonyKl98 commented 6 months ago

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What happened?

Script contains QCmetrics$Cell.type, however the standard name is Cell_Type. Running the script as it currently is, it normalised all my samples together rather than normalising the cell types separately. When loading in the normalised data, the object is called normbeta rather than celltypeNormbeta. Could cell.type be corrected to Cell_Type, or ensure it matches what is on your sample sheet so that it normalises the cell types separately and gives celltypeNormbeta?

How can the bug be reproduced?

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Relevant log output

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alicemfr commented 6 months ago

Currently the normalisation is performed across all samples first and then within cell-type. We could jump straight to within cell-type by utilising the cellSorted=TRUE argument in the config.r file.

ejh243 commented 5 months ago

This is will partly be resolved by the script to check format of sample sheet (& config file). links to #32