Gardenia_3859

@火卫控 谢谢已解决

R 读取单细胞H5ad数据

R 读取单细胞H5ad数据， 转换为Seurat能直接读取的对象 运行情况 需要一会儿时间，H5ad源文件大约 10GB 左右

火卫控

7359 5 1

Gardenia_3859

@TOP生物信息 肿瘤细胞都根据患者的不同独立成群 那后续能分析细胞互作吗？有意义吗？

单细胞分析实录(6): 去除批次效应/整合数据

上一篇已经讲解了Seurat标准流程，推文的最后，注意到了不同样本之间的表达数据是存在批次效应的，就像下图这样，有些是可以聚到一起的亚群，却出现了不同样本分开/偏移的情况，比...

TOP生物信息

24715 25 35

Gardenia_3859

> Convert('D:/DraftR/cell intersection/02-cell-cell/08-bulk层面验证细胞互作/01-TAM_Tregs/03_scTenifold_adata_merge_example.h5ad', "h5seurat",overwrite = TRUE,assay = "RNA")
警告: Unknown file type: h5ad
Creating h5Seurat file for version 3.1.5.9900
Adding X as scale.data
Adding X as data
Adding X as counts
Adding meta.features from var
Adding X_pca as cell embeddings for pca
Adding X_umap as cell embeddings for umap
Adding layer log1p as data in assay log1p
Adding layer raw as data in assay raw
> scTenifold_data <- LoadH5Seurat("D:/DraftR/cell intersection/02-cell-cell/08-bulk层面验证细胞互作/01-TAM_Tregs/03_scTenifold_adata_merge_example.h5seurat")
Validating h5Seurat file
Initializing RNA with data
Adding counts for RNA
Adding scale.data for RNA
Adding feature-level metadata for RNA
Initializing log1p with data
Initializing raw with data
警告: Layer counts isn't present in the assay object; returning NULL
警告: Layer counts isn't present in the assay object; returning NULL
Adding reduction pca
Adding cell embeddings for pca
Adding miscellaneous information for pca
Adding reduction umap
Adding cell embeddings for umap
Adding miscellaneous information for umap
Adding command information
Adding cell-level metadata
错误: Missing required datasets 'levels' and 'values'
>
你好请问这要怎么解决？

R 读取单细胞H5ad数据

R 读取单细胞H5ad数据， 转换为Seurat能直接读取的对象 运行情况 需要一会儿时间，H5ad源文件大约 10GB 左右

火卫控

7359 5 1