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Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas

Code repository for the Tumor Immune Cell Atlas (TICA) project
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error when loading TICAtlas.h5ad data #2

Closed Byronxy closed 3 years ago

Byronxy commented 3 years ago

Hi, I download the data from zenodo while I find the error when load data.

  1. load data in R I use the following code:

    Convert("~/software/TICAtlas.h5ad", dest = "h5seurat", overwrite = TRUE)
TICAtlas <- LoadH5Seurat("~/software/TICAtlas.h5seurat")

    The error is Validating h5Seurat file Initializing RNA with data Adding counts for RNA Adding scale.data for RNA Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

  2. load data in python I use the following code:

    import scanpy as sc
adata = sc.read_h5ad("/export/bioinfo-team/home/xiongy/software/TICAtlas.h5ad")

    The error is ValueError: Variables annot.varmust have number of columns ofX(5000), but has 4997 rows.

sialindskrog commented 3 years ago

I got the same error.

However, it worked when only including the count and data assays (excluding the scale.data assay): tica <- LoadH5Seurat("/Data/TICAtlas.h5seurat", assays = c("counts", "data"))

But a solution to load the entire dataset would of course be optimal.

PaulaNietoG commented 3 years ago

Hi! Thanks for letting us know! We are working on fixing this as soon as possible

PaulaNietoG commented 3 years ago

This should now be fixed in the latest Zenodo upload (https://doi.org/10.5281/zenodo.4036019)