Comments (2)
Syksy
commented on July 30, 2024
The ERG fusion status has been determined using gene expression; for some samples, only gene expression has been determined, while for others copy number alterations are available. We don't have full coverage over all omics.
MultiAssayExperiment does support operations that do pick samples that have information available; using some of the MAE-object functionality may prove useful: https://www.bioconductor.org/packages/devel/bioc/vignettes/MultiAssayExperiment/inst/doc/QuickStartMultiAssay.html
I'm yet to explore all of the options myself, but they seem to have covered it rather nicely. If there are some samples which should have CNA data but don't have it in the MAE-object, then those we can try fill - but it can also be that GDC (where we pull GEX and CNA data from) never processed them.
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MikeOrman
commented on July 30, 2024
Awesome, i'll take a closer look at the vignette. Thank you for the clarification!
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Related Issues (20)
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