`norm.factors` not being transferred from `SpatialExperiment` to `DGEList`
jaredmcollette opened this issue · comments
When using TMM normalisation on a spatial experiment object using geomxNorm()
, the norm.factors
are stored in the metadata.
Later, when using SE2DGEList()
to convert the spatial experiment object to a dgeList, the norm.factors
are not automatically carried over to the dge
, and I have to manually transfer over the norm.factors
:
dge$samples$norm.factors <- metadata(spe_tmm)$norm.factor
It would be helpful to have this process automated
Hi @jaredmcollette , thanks for the suggestion. The SE2DGEList
is from the edgeR package, hence wouldn't aware any of the metadata we stored in the spe. I'll probably write a new function to replace SE2DGEList
before the next release to incorporate the suggested ability.