Test if GeomxSet works with available DE packages

Nanostring-Biostats / GeomxTools

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.

MIT License

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Test if GeomxSet works with available DE packages #21

Open rvitancol opened 3 years ago

rvitancol commented 3 years ago

Check if GeomxSet works with available DE packages:

[x] limma
[ ] DESeq2
[ ] EdgeR

Check if we need to create adapter functions to use these.

NicoleEO commented 3 years ago

I confirmed this works with limma: fit <- lmFit(exprs(object), model.matrix(design(object), sData(object))) fit <- eBayes(fit) DE_table <- topTable(fit, coef=2, adjust="fdr", n=5)