Closed lcolladotor closed 1 year ago
After reading the docs for SPOTlight, @Nick-Eagles @lahuuki and me agree what we should use all the data since they do say you do need more if your cell types are related, which is the case in our layer-level analysis.
https://bioconductor.org/packages/release/bioc/vignettes/SPOTlight/inst/doc/SPOTlight_kidney.html
See https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1671588769748179 for the full description.
Basically, over the winter break it'd be nice to have
SPOTlight
re-run using:caracol
if it needs lots of memory)set.seed()
call to make the results reproducible.Aka, a
set.seed()
before https://github.com/LieberInstitute/spatialDLPFC/blob/1b4d8e7161be2310af87b88ed8e167ffedb99098/code/spot_deconvo/04-spotlight/02-nonIF.R#L145-L146 if needed. Or well, avoid https://github.com/LieberInstitute/spatialDLPFC/blob/1b4d8e7161be2310af87b88ed8e167ffedb99098/code/spot_deconvo/04-spotlight/02-nonIF.R#L60 altogether.(Applies for both IF and non-IF data)
Thanks!