-
Here is a reproducible code for the error:
```
import scanpy as sc
import scanpy.external as ice
from itertools import cycle
pbmc = sc.datasets.pbmc68k_reduced()
pbmc_corrected = mnnpy.mnn_c…
-
Hi Aaron,
Do you think it is appropriate to use MNN corrected data for diffusion map formation too?
Thank you for your help.
-
Hi mnnpy,
I am getting an error using mnnpy.mnn_correct and wondering if you could please comment on my error. I have the latest version of numba and llvmlite.
Here is what I used:
```
adata_lis…
-
1、windows系统下，cpu推理正常，AMD核显opencl推理结果错误，使用MNN版本为2.8.1
cpu推理结果：
opencl推理结果：
```
Performing cosine normalization...
Starti…
-
Hi MNN group,
I see in the MNN help pages that it is not recommended to use MNN-corrected gene expression matrix for quantitative analysis such as differential gene expression. But I wonder if it i…
-
Dear Chris,
I posted this to the SCANPY Github repo but they directed me to you.
Any ideas what could be causing this [error](https://github.com/theislab/scanpy/issues/1167#issue-601302612)
Tha…
-
>>> corrected = mnnpy.mnn_correct(a,b,var_index=gene, var_subset=hvgs, batch_categories = ["A", "B"], cos_norm_out=False)
Inputs are AnnData objects, var_index ignored.
Performing cosine normalizati…
-
The default value of `var_index` is `None`, but the first thing you do with it if the data is not `AnnData` is take the `len`. https://github.com/chriscainx/mnnpy/blob/master/mnnpy/mnn.py#L148
```
…
-
Hey there,
I'm running mnn_correct on 5 AnnData batches. I'm finding that with either svd_mode='svd' or svd_mode='rsvd', I am geting the same error posted below. I can assure you, the inputted data…