Closed faridrashidi closed 1 year ago
Hi, Thank you for using XClone. Maybe you can have a look at the tutorial TNBC1 dataset (10x) (details of params are shown in the tutorial).
And could you please show me the log of xconfig.display()
?
Thank you for your help. I get the same error when running the TNBC1 example. Here's the log of xconfig for the TNBC1 example:
RDR
Configurations:
HMM_brk chr_arm
KNN_neighbors 10
WMA_smooth_key chr_arm
WMA_window_size 40
_file_format_data h5ad
_file_format_figs pdf
_frameon True
_outdir .
_plot_suffix
_start 1682306587.118832
_vector_friendly True
cell_anno_key cluster.pred
dataset_name TNBC1_scRNA
dispersion_celltype None
exclude_XY False
file_format_data h5ad
file_format_figs pdf
filter_ref_ave 0.5
fit_GLM_libratio False
gene_exp_group 1
gene_exp_ref_log True
guide_chr_anno_key chr_arm
guide_cnv_ratio None
guide_qt_lst [0.0001, 0.96, 0.99]
marker_group_anno_key cluster.pred
max_iter 2
min_iter 1
module RDR
outdir .
plot_cell_anno_key cluster
plot_suffix
rdr_plot_vmax 0.7
rdr_plot_vmin -0.7
ref_celltype N
remove_guide_XY False
remove_marker True
select_normal_chr_num 4
set_figtitle True
set_smartseq False
smart_transform False
start_prob [0.1 0.8 0.1]
top_n_marker 15
trans_prob [[9.99998e-01 1.00000e-06 1.00000e-06]
[1.00000e-06 9.99998e-01 1.00000e-06]
[1.00000e-06 1.00000e-06 9.99998e-01]]
trans_t 1e-06
warninig_ignore True
xclone_plot True
P.S. I use python v3.9.2 and XClone v0.3.4
Hi, Could you have a try on python 3.7 and XClone v0.3.4?
Thank you, Rongting, for your assistance in resolving the issue. It seems XClone only works with Python 3.7. I tried running it with Python 3.8.10 and 3.9.2, but encountered the same issue. I appreciate your help in pointing me in the right direction.
I have two more questions before closing this issue:
1) Can XClone detect tumor and normal cells without any prior information itself?
2) It seem filter_ref_ave
parameter is an important factor in determining the CNV which is set to 0.5 as default. Is there any way to adjust this variable accordingly to the data e.g. based on library size?
Hi @faridrashidi, thank you for your feedback! XClone is stable in Python 3.7 (3.8 and 3.9 may cause some issues in xclone's requirement packages, we will test later).
filter_ref_ave
parameter is an important factor, but here it is just a parameter that helps to do gene filtering at the first step. if the average gene value in reference cells is too low, then the gene will be discarded. In 10x seq data, we set it to 0.5 as default to keep 3000~6000 genes for analysis.Thank you very much!
Hi, @faridrashidi, could you help to provide the scanpy
version in your Python 3.8.10 and 3.9.2 env?
For 3.8.10 is v1.9.2 For 3.9.2 is v1.9.1
Hi, @Rongtingting, could you please send me the example for finding normal and tumor cells by XClone that you mentioned here?
Hi,
I'm trying to run XClone RDR module following scripts at here on a dataset but I get the following error:
Could you please help me what I should do to resolve this issue?