Hello everyone, I am new to bioinformatics and want to build a reference atlas to project my own data on it using scArches and other packages like scanpy. However, I'm having troubles in loading the reference dataset . I downloaded the exprMatrix.tsv.gz file from https://cells-test.gi.ucsc.edu/?ds=early-brain and used the following code to import the data into Python:
import scanpy as sc adata = sc.read_text("exprMatrix.tsv.gz")
I get this error:
ValueError: could not convert string to float: 'NA'
I tried loading the data in R with the Seurat package, which worked after appending one empty line. Can it be that Python and R use different expressions for 'NA' values (NaN?) and therefore Python can not load the file? Can I just replace the 'NA' values with 'NaN' in the file or do they have a different meaning?
I would very much appreciate help. Thank you for taking the time!