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cnk113 / vascular-analysis

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Mixed up data on UCSC Cell Browser? #1

Open simonmfr opened 1 year ago

simonmfr commented 1 year ago

Hi,

looking at UCSC cell browser I found that the exprMatrix.tsv.gz file "Adult Brain Endothelial" seems to be a raw count matrix, whereas the "Adult Brain Perivascular" dataset seems to be a log-transformed matrix. That is unexpected - can you please confirm?

Expression of 100 random genes:

Many thanks, Simon

zerostwo commented 11 months ago

Hi,

looking at UCSC cell browser I found that the exprMatrix.tsv.gz file "Adult Brain Endothelial" seems to be a raw count matrix, whereas the "Adult Brain Perivascular" dataset seems to be a log-transformed matrix. That is unexpected - can you please confirm?

Expression of 100 random genes:

  • Endothelial: image
  • Perivascular: image

Many thanks, Simon

The website seems to provide the data after sctransform, without the original counts.

shanshenbing commented 6 months ago

Any suggestions? Hope anyone gets some help.