Which batch corrected data should be used in pbmc_gene_expression dataset?

3rd (Public) Challenge
1

I’ve noticed that the pbmc_gene_expression dataset doesn’t contain batchCorrected_data as others. However, there is a batch corrected data under both raw_count and TPM data in gene expression data. Could you please provide further instructions on how to proceed with this particular dataset?

2

Hi @Yiran_Liu,

Thank you for your query. We performed batch effect correction separately on the TPM and raw count data. You should see the batch-corrected data if you open the TPM data (e.g., TPM@). Please also refer steps mentioned here to know details.

Please let me know if you encounter any further issues.

Best,
Pramod