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Gardenia_3859

@火衛(wèi)控 謝謝已解決

R 讀取單細(xì)胞H5ad數(shù)據(jù)

R 讀取單細(xì)胞H5ad數(shù)據(jù)， 轉(zhuǎn)換為Seurat能直接讀取的對象 運行情況 需要一會兒時間，H5ad源文件大約 10GB 左右

火衛(wèi)控

7747 5 1

Gardenia_3859

@TOP生物信息 腫瘤細(xì)胞都根據(jù)患者的不同獨立成群 那后續(xù)能分析細(xì)胞互作嗎？有意義嗎？

單細(xì)胞分析實錄(6): 去除批次效應(yīng)/整合數(shù)據(jù)

上一篇已經(jīng)講解了Seurat標(biāo)準(zhǔn)流程，推文的最后，注意到了不同樣本之間的表達數(shù)據(jù)是存在批次效應(yīng)的，就像下圖這樣，有些是可以聚到一起的亞群，卻出現(xiàn)了不同樣本分開/偏移的情況，比...

TOP生物信息

25297 25 35

Gardenia_3859

> Convert('D:/DraftR/cell intersection/02-cell-cell/08-bulk層面驗證細(xì)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層面驗證細(xì)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
錯誤: Missing required datasets 'levels' and 'values'
>
你好請問這要怎么解決？

R 讀取單細(xì)胞H5ad數(shù)據(jù)

R 讀取單細(xì)胞H5ad數(shù)據(jù)， 轉(zhuǎn)換為Seurat能直接讀取的對象 運行情況 需要一會兒時間，H5ad源文件大約 10GB 左右

火衛(wèi)控

7747 5 1