今天跑DCA的代码时,发现了这个问题,我发现DCA模型的模拟数据集无法存储。发生错误
adata = sc.AnnData(counts.values, obs=cellinfo, var=geneinfo)
adata.obs_names = cellinfo.Cell
adata.var_names = geneinfo.Gene
#adata.obs.index = list(adata.obs.index) ## add this line to avoid error
#adata.var.index = list(adata.var.index) ## add this line to avoid error
sc.pp.filter_genes(adata, min_counts=1)
adata.write("./fig2_simulation_2group.h5ad")
adata
解决办法:
https://github.com/scverse/anndata/issues/452
修改代码如下
adata = sc.AnnData(counts.values, obs=cellinfo, var=geneinfo)
adata.obs_names = cellinfo.Cell
adata.var_names = geneinfo.Gene
adata.obs.index = list(adata.obs.index) ## add this line to avoid error
adata.var.index = list(adata.var.index) ## add this line to avoid error
sc.pp.filter_genes(adata, min_counts=1)
adata.write("./fig2_simulation_2group.h5ad")
adata
结果如下