cNMF

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IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

7

Hi, I am getting this error, I tried reinstalling but couldn't resolve this issue. I have removed all the low counts and even tried giving TPMs, but failed in running...

AteeqMKhaliq

The nmf running error on python3.7.13 version

2

Hi guys, When i running the cnmf， the error showing up lying below: ValueError: Distance matrix 'X' must be symmetric. miniconda environment python 3.7.13 Best

honghh2018

applying cNMF to multiple datasets?

9

How would you recommend to proceed with multiple samples? In the original manuscript, you conclude that it is better to perform any kind of batch correction before applying cNMF, correct?

erzakiev

Nan issue when linearly regressing out batch and zeroing negative values

1

Hi, I wanted to try linearly regressing out batch from a TPM counts matrix and then zeroing negative values as the input for cNMF. I am getting the following error:...

carversh

multi-proccessing from script?

3

Hi, first, thank you for providing this tools to the community. I was wondering if there is any way to use multiprocessing from inside a script? Looking at the code...

rLannes

ValueError: shapes (7,78103) and (56262,999) not aligned: 78103 (dim 1) != 56262 (dim 0)

9

Hello, I was following one of the tutorials for running cNMF on my own data set. My dataset has 78103 observations and on NAs or inf counts. To see if...

johnjeang

error in the tutorial: "high is out of bounds for int32"

4

Hello, When running the tutorial notebook analyze_pbmc_example_data.ipynb I get the following error: > ValueError Traceback (most recent call last) ~\AppD``` > ata\Local\Temp\ipykernel_25820\2126166754.py in > 1 ## Prepare the data, I.e....

ronamit

no top_genes in outputs

4

Hi, I am running version 4.1 in command line and I am getting all the output, except for top_genes. Do you know if there is something I can do to...

DiegoSafian

Discrepancies in 'k' Output: Command Line vs. Python Environment

4

Hi Dylan! Yesterday I ran the cNMF in the terminal (Mac M1) and everything went smoothly until the final step, where I encountered an unusual error: ``` (py37) Mac-Studio-de-Maria:tables marialuciaromerorivero$...

mluciarr

HI, I was wondering if there is an advisable way to incorporate the usage result into a Seurat object (ideally V5), so that one can calculate the usage of GEP...

DiegoSafian