PyDeseq2 - InvalidIndexError
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5 days ago
tmanjonas • 0

Hey everyone, im currently trying to use PyDeseq2 on bulk RNA-seq data, but i keep getting this error Error msg when running the dds.deseq2().

This is my metadata: Metadata

And this my counts: counts

Shouldnt the indices of both tables be the same to correctly match samples with condition ?

Id appreciate any help. Thanks :)

python rna-seq pandas pydeseq2 deseq2 • 285 views
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You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae. Take a look at comments on this post for some help: https://stackoverflow.com/q/77251779 .

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