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16 days ago • updated 3 days ago
Jenny Drnevich
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2.0k
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updated 4 months ago by
Michael Love
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written 4 months ago by
Aditya
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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
by
Guandong Shang
▴
20
Thanks for your reply, Aaron :)
Answer: `emptyDrops()` calling 'too many' non-empty droplets
by
Aaron Lun
★
27k
Perhaps there is something wonky with the TCR sequences that exclude them from the barcodes with below 100 counts. Maybe TCR sequences are …
Answer: how to do downstram analysis to cells which are subsetted after MNN batch-correc
by
Aaron Lun
★
27k
In this case, you can just replace `denoisePCA` in the example with the various MNN steps. So:
```
# NOTE: not tested!
sce.sub <- sce[…
Answer: how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more rea
by
Aaron Lun
★
27k
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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