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Nanostring-Biostats / GeoDiff

GeoDiff, an R package for count generating models for analyzing Geomx RNA data. Note that this version of the package is still under development, undergoing submission process to Bioconductor 3.14 release and still needs to complete NanoString internal verification process.
MIT License
7 stars 6 forks source link

Updated Vignette #13

Closed maddygriz closed 2 years ago

maddygriz commented 2 years ago

Updated vignette, need to check for correct statistical descriptions and ease of use for a biologist.

zhiiiyang commented 2 years ago

@maddygriz, could you resolve the conflict files?

maddygriz commented 2 years ago

no errors or warnings from devtools::check(vignettes =TRUE)

stzimmerman commented 2 years ago

Looks really good Maddy! Just a few comments and suggested text edits:

  1. In the aggreprobe section, this sentence isn't clear to me "...probes get filtered based on either correlation and/or the score test." It seems like probes are being aggregated not filtered here?
  2. "Using the background score test, we can determine which probes are above background. To subsample the data to just the probes above background, keep probes with a p-value less than 1e-3." -> "Using the background score test, we can determine which targets are expressed above the background of the negative probes across this dataset. We can then filter the data to only targets above background, using a suggested pvalue threshold of 1e-3."
    1. split - should the split poisson background values be used -> "should the poisson background values split by group be used"
  4. "To filter out poor quality ROIs, we only keep those which have a high enough threshold." - threshold of what?
  5. Can the relation between models plots have better axis labels than xlab = "Fixed Effect model" and ylab = "Mixed Effect Model"? I'm confused about what's actually being compared
  6. It might be nice to have a little more explanation of what the sizeratio is in the PCA plots. I can see the calculation, I just don't totally understand what it means intuitively
zhiiiyang commented 2 years ago

It passed devtools::check()