Hello, and thank you for developing Libra — it is extremely useful for pseudobulk-based DE analysis.
While running pseudobulk DE using DESeq2 backend, I noticed that the resulting output does not contain the Wald statistic (stat) or lfcSE, although DESeq2 normally provides these values.
Is there a recommended way to access the original DESeq2 results, including:
baseMean
lfcSE
stat (Wald statistic)
and any other DESeq2-native fields
when using Libra’s pseudobulk DE with de_family = "deseq2"?
For example, is there an argument (e.g. return_fit or similar) or a documented accessor that allows me to retrieve the underlying DESeqDataSet / results() output used internally by Libra?
Thank you again for your work on this package!
Hello, and thank you for developing Libra — it is extremely useful for pseudobulk-based DE analysis.
While running pseudobulk DE using DESeq2 backend, I noticed that the resulting output does not contain the Wald statistic (stat) or lfcSE, although DESeq2 normally provides these values.
Is there a recommended way to access the original DESeq2 results, including:
baseMean
lfcSE
stat (Wald statistic)
and any other DESeq2-native fields
when using Libra’s pseudobulk DE with de_family = "deseq2"?
For example, is there an argument (e.g. return_fit or similar) or a documented accessor that allows me to retrieve the underlying DESeqDataSet / results() output used internally by Libra?
Thank you again for your work on this package!