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Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
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Comment: Detection of reference genes by Deseq2
by
ATpoint
★
1.4k
Long story short, use `plotMA()` to see how normalization went. If the plot is somewhat symmetric and/or the majority of point center along…
Comment: how to do downstram analysis to cells which are subsetted after MNN batch-correc
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Thanks for your reply, Aaron :)
Answer: `emptyDrops()` calling 'too many' non-empty droplets
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★
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Perhaps there is something wonky with the TCR sequences that exclude them from the barcodes with below 100 counts. Maybe TCR sequences are …
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★
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In this case, you can just replace `denoisePCA` in the example with the various MNN steps. So:
```
# NOTE: not tested!
sce.sub <- sce[…
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It is, in general, difficult to interpret the `reconstructed` assay, as batch correction is not guaranteed to do "sensible" things to the p…
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