Comments (5)
It looks like you did not change the filtering thresholds. It's possible that cells are being filtered out, depending on their value. What if you specify -F
?
from too-many-cells.
Thanks for the reply. I check the workshop at https://gregoryschwartz.github.io/too-many-cells/workshop/workshop.html, didn't find what -F means? Do you mean --filter-thresholds? I add --filter-thresholds "(250, 1)" \ and try
vip06@tpm5-desktop:~$ docker run -it --rm -v "/home/data/vip06:/home/data/vip06" gregoryschwartz/too-many-cells:2.0.0.0 make-tree --matrix-path /home/data/vip06/scdata/allraw/day14 --labels-file /home/data/vip06/labels.csv --filter-thresholds"(250, 1)" --output /home/data/vip06/result/
Invalid option --filter-thresholds(250, 1)' it showed no Invalid option
--filter-thresholds(250, 1)'
from too-many-cells.
-F
is from older versions which I think that docker uses. You can customize the --filter-thresholds
argument to make sure no filtering is done (I don't know what your data looks like so I don't know if it's normalized or has some other kind of count data).
from too-many-cells.
Also, you need a space in your argument --filter-thresholds "(250, 1)"
, but also you should choose different numbers to be lower depending on your data.
from too-many-cells.
Closing due to inactivity.
from too-many-cells.
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from too-many-cells.