Invalid Counts data

[zhuyewen]

Hello, cellphonedb team!

Thank you very much for open sourcing such a great single cell tool. I have been using it from 3.0 until now 4.0 and it has helped me a lot.

But in the recent 4.0, I have encountered some problems. I can work fine using the data you provided. But when using my own data, it prompts an error.

I input these data like this:

cpdb_file_path = '/Users/zhuyewen/Downloads/CellphoneDB-master/db/v4.1.0/cellphonedb.zip'

meta_file_path = '/Users/zhuyewen/R/技术摸索/23.cellphonedb/metadata.tsv'
counts_file_path = '/Users/zhuyewen/R/技术摸索/23.cellphonedb/pbmc3k.h5ad'

out_path = '/Users/zhuyewen/Downloads/CellphoneDB-master/result/method2'

...

from cellphonedb.src.core.methods import cpdb_statistical_analysis_method

deconvoluted, means, pvalues, significant_means = cpdb_statistical_analysis_method.call(
    cpdb_file_path = cpdb_file_path,                 # mandatory: CellPhoneDB database zip file.
    meta_file_path = meta_file_path,                 # mandatory: tsv file defining barcodes to cell label.
    counts_file_path = counts_file_path,             # mandatory: normalized count matrix.
    counts_data = 'hgnc_symbol',                     # defines the gene annotation in counts matrix.
#     microenvs_file_path = microenvs_file_path,       # optional (default: None): defines cells per microenvironment.
    iterations = 1000,                               # denotes the number of shufflings performed in the analysis.
    threshold = 0.1,                                 # defines the min % of cells expressing a gene for this to be employed in the analysis.
    threads = 4,                                     # number of threads to use in the analysis.
    debug_seed = 42,                                 # debug randome seed. To disable >=0.
    result_precision = 3,                            # Sets the rounding for the mean values in significan_means.
    pvalue = 0.05,                                   # P-value threshold to employ for significance.
    subsampling = False,                             # To enable subsampling the data (geometri sketching).
    subsampling_log = False,                         # (mandatory) enable subsampling log1p for non log-transformed data inputs.
    subsampling_num_pc = 100,                        # Number of componets to subsample via geometric skectching (dafault: 100).
    subsampling_num_cells = 1000,                    # Number of cells to subsample (integer) (default: 1/3 of the dataset).
    separator = '|',                                 # Sets the string to employ to separate cells in the results dataframes "cellA|CellB".
    debug = False,                                   # Saves all intermediate tables employed during the analysis in pkl format.
    output_path = out_path,                          # Path to save results.
    output_suffix = None                             # Replaces the timestamp in the output files by a user defined string in the  (default: None).
    )

And I got this error

ParseCountsException: Invalid Counts data

Here's how I generated the expression matrix file in Rstudio

library(SeuratDisk)
library(Seurat)

SaveH5Seurat(pbmc3k.final, filename = "pbmc3k.h5Seurat")
Convert("pbmc3k.h5Seurat", dest = "h5ad",assay = 'RNA')

I am not sure if there is something wrong with the code I used to generate the h5ad file, if so could you please provide the code on how to generate that file using R language?

I browsed through all the issues and found no similar questions or answers. I hope you have time to tell me how to generate h5ad from Seurat object by R, and hopefully provide a solution for people who encounter the same problem later. Thanks a lot.

My platform: MacOs13.3, Apple M1 Ultra, R version 4.3.0, python = 3.8

Best regard

Yewen Zhu

[ktroule]

Hi.

We have this notebook on how to convert your seurat object for CellPhoneDB. Other option, can be the use of sceasy to convert from seurat to scanpy.

Kind regards

[luzgaral]

Hi,

Also, you can use the strategies mentioned here (how-to-extract-the-cellphonedb-input-files-from-a-seurat-object) to convert Seurat objects into formats accepted by CellPhoneDB.

Best

Luz