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Negative values after pt.pp.dsb #116

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ChaseTaylor939 opened this issue Jul 28, 2023 · 1 comment
Open

Negative values after pt.pp.dsb #116

ChaseTaylor939 opened this issue Jul 28, 2023 · 1 comment
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bug Something isn't working

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@ChaseTaylor939
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Describe the bug
Lots of my CITE-seq values are negative after running pt.pp.dsb. It seems like like they shouldn't be below 0. Am I just misunderstanding how pt.pp.dsb works?

To Reproduce

BAL_9282_JC_1 = mu.read_10x_h5('/home/taylor81/BAL_Data/9282-JC-1/ec5337_tdi30000_fpr_0.01_epochs150_filtered.h5')
BAL_9282_JC_1_raw = mu.read_10x_h5('/home/taylor81/BAL_Data/9282-JC-1/raw_feature_bc_matrix.h5')
pt.pp.dsb(BAL_9282_JC_1,BAL_9282_JC_1_raw,random_state = 1)

Expected behaviour
I would expect no negative values, but I get negative values like the following example:

<style> </style>
  Hu.CD101 Hu.CD103 Hu.CD105_43A3 Hu.CD107a Hu.CD112 Hu.CD119 Hu.CD11a Hu.CD11b Hu.CD11c Hu.CD122 Hu.CD123 Hu.CD124 Hu.CD127 Hu.CD13
CTGATCCCAATGGACG-1 -10.224 10.86788 -3.03904 -42.3412 -8.69139 -7.74294 -42.4369 -13.9509 -34.5928 -3.91137 -21.7118 -9.87767 -7.54718 9.31312

System

  • OS: 5.19.0-35-generic
  • Python 3.10.9

Package Version Editable project location


absl-py 1.4.0
adjustText 0.8
aiohttp 3.8.4
aiosignal 1.3.1
airr 1.4.1
alabaster 0.7.13
anndata 0.9.1
annoy 1.17.1
anyio 3.5.0
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.5
async-timeout 4.0.2
attrs 22.1.0
awkward 2.2.3
awkward-cpp 17
Babel 2.11.0
backcall 0.2.0
bbknn 1.5.1
beautifulsoup4 4.11.1
bleach 4.1.0
boltons 23.0.0
Bottleneck 1.3.5
brotlipy 0.7.0
cached-property 1.5.2
cellbender 0.2.2 /home/taylor81/CellBender
celltypist 1.3.0
certifi 2022.12.7
cffi 1.15.1
charset-normalizer 2.0.4
chex 0.1.7
click 8.0.4
colorama 0.4.6
comm 0.1.2
conda 23.3.1
conda-package-handling 2.0.2
conda_package_streaming 0.7.0
contextlib2 21.6.0
contourpy 1.0.5
cryptography 39.0.1
cycler 0.11.0
Cython 0.29.33
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
dm-tree 0.1.8
docrep 0.3.2
docutils 0.18.1
entrypoints 0.4
et-xmlfile 1.1.0
etils 1.2.0
executing 0.8.3
fastjsonschema 2.16.2
filelock 3.9.0
flax 0.6.9
flit_core 3.8.0
fonttools 4.25.0
frozenlist 1.3.3
fsspec 2023.5.0
future 0.18.3
gmpy2 2.1.2
h5py 3.7.0
harmonypy 0.0.9
idna 3.4
igraph 0.9.11
imageio 2.26.0
imagesize 1.4.1
importlib-metadata 6.0.0
importlib-resources 5.12.0
ipykernel 6.19.2
ipython 8.10.0
ipython-genutils 0.2.0
ipywidgets 7.6.5
jax 0.4.8
jaxlib 0.4.7
jedi 0.18.1
Jinja2 3.1.2
joblib 1.1.1
json5 0.9.6
jsonpatch 1.32
jsonpointer 2.1
jsonschema 4.17.3
jupyter 1.0.0
jupyter_client 8.1.0
jupyter-console 6.4.4
jupyter_core 5.3.0
jupyter-server 1.23.4
jupyterlab 3.5.3
jupyterlab-pygments 0.1.2
jupyterlab_server 2.19.0
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
lazy_loader 0.1
leidenalg 0.8.10
Levenshtein 0.21.1
lightning-utilities 0.8.0
llvmlite 0.39.1
loompy 3.0.6
louvain 0.8.0
lxml 4.9.1
markdown-it-py 2.2.0
MarkupSafe 2.1.1
matplotlib 3.6.2
matplotlib-inline 0.1.6
mdurl 0.1.2
mistune 0.8.4
mizani 0.9.2
mkl-service 2.4.0
ml-collections 0.1.1
ml-dtypes 0.1.0
mock 4.0.3
mofapy2 0.7.0
mofax 0.3.6
mpmath 1.2.1
msgpack 1.0.5
mudata 0.2.3
multidict 6.0.4
multipledispatch 0.6.0
munkres 1.1.4
muon 0.1.5
natsort 7.1.1
nbclassic 0.5.2
nbclient 0.5.13
nbconvert 6.5.4
nbformat 5.7.0
nest-asyncio 1.5.6
networkx 2.8.4
notebook 6.5.2
notebook_shim 0.2.2
numba 0.56.4
numexpr 2.8.4
numpy 1.23.5
numpy-groupies 0.9.20
numpyro 0.11.0
openpyxl 3.1.1
opt-einsum 3.3.0
optax 0.1.5
orbax-checkpoint 0.2.2
packaging 23.0
pandas 1.5.3
pandocfilters 1.5.0
parasail 1.3.4
parso 0.8.3
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 23.0.1
platformdirs 2.5.2
plotnine 0.12.1
pluggy 1.0.0
ply 3.11
pooch 1.7.0
prometheus-client 0.14.1
prompt-toolkit 3.0.36
protobuf 3.20.3
psutil 5.9.0
ptyprocess 0.7.0
pure-eval 0.2.2
pycosat 0.6.4
pycparser 2.21
Pygments 2.14.0
pynndescent 0.5.4
pyOpenSSL 23.0.0
pyparsing 3.0.9
PyQt5-sip 12.11.0
pyro-api 0.1.2
pyro-ppl 1.8.4
pyrsistent 0.18.0
pysam 0.20.0
PySocks 1.7.1
python-dateutil 2.8.2
python-igraph 0.10.4
python-Levenshtein 0.21.1
pytorch-lightning 1.9.5
pytz 2022.7
PyWavelets 1.4.1
PyYAML 6.0
pyzmq 23.2.0
qtconsole 5.4.0
QtPy 2.2.0
rapidfuzz 3.1.1
requests 2.28.1
rich 13.3.5
ruamel.yaml 0.17.21
ruamel.yaml.clib 0.2.6
scanpy 1.9.3
scikit-image 0.20.0
scikit-learn 1.2.0
scikit-misc 0.2.0
scipy 1.9.3
scirpy 0.13.0
scrublet 0.2.3
scvi-colab 0.12.0
scvi-tools 0.20.3
seaborn 0.12.2
Send2Trash 1.8.0
session-info 1.0.0
setuptools 65.6.3
sip 6.6.2
six 1.16.0
sniffio 1.2.0
snowballstemmer 2.2.0
soupsieve 2.3.2.post1
Sphinx 6.1.3
sphinx-argparse 0.4.0
sphinx_autodoc_typehints 1.22
sphinx-rtd-theme 1.2.0
sphinxcontrib-applehelp 1.0.4
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.1
sphinxcontrib-jquery 4.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-programoutput 0.17
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
squarify 0.4.3
stack-data 0.2.0
statsmodels 0.14.0
stdlib-list 0.8.0
sympy 1.11.1
tables 3.7.0
tensorstore 0.1.36
terminado 0.17.1
texttable 1.6.4
threadpoolctl 2.2.0
tifffile 2023.2.28
tinycss2 1.2.1
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
torch 1.13.1
torchaudio 0.13.1
torchmetrics 0.11.4
torchvision 0.14.1
tornado 6.2
tqdm 4.65.0
traitlets 5.7.1
typing_extensions 4.4.0
umap-learn 0.5.3
urllib3 1.26.15
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 0.58.0
wheel 0.38.4
widgetsnbextension 3.5.2
xlrd 1.2.0
yamlordereddictloader 0.4.0
yarl 1.9.2
zipp 3.11.0
zstandard 0.19.0

Additional context
Add any other context about the problem here.

@ChaseTaylor939 ChaseTaylor939 added the bug Something isn't working label Jul 28, 2023
@racng
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racng commented Sep 5, 2023

Looking at the publication for the dsb tool, Figure 4a shows some negative values for dsb normalized protein data. So it seems like we should expect some negative values. Link to figure: https://www.nature.com/articles/s41467-022-29356-8/figures/4

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