Error of Link_pathway_blocks_gwas

sulab-wmu / scPagwas

Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data

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Open zywz12138 opened 4 months ago

zywz12138 commented 4 months ago

当我进行到Link_pathway_blocks_gwas这步操作的时候，我遇到了以下问题，请问应该如何解决，谢谢

Start to link gwas and pathway block annotations for 327 pathways! | | 0%Creating directory "./temp" which didn't exist.. |=== | 4%Error in svd(covar.train, nv = 0) : infinite or missing values in 'x'

dengchunyu commented 2 months ago

你这个也是单细胞数据质量的问题，有缺失值或者无穷值，这种情况在大多数单细胞的软件包中都是会报这种错误的。最好重新读取单细胞count数据，重新进行预处理，保证流程正确