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zhouhj1994 / LinDA

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Linda not working #14

Open mradz19 opened 9 months ago

mradz19 commented 9 months ago

I am trying to run Linda on my data, I have an otu matrix (called genus) with the taxa as rownames and sampleIDs as column names and a metdata df with the sampleIds as the rownames.

I get this error:

linda(genus, metadata, formula = '~ Pathology*Antibiotics')
Pseudo-count approach is used.
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent

I have confirmed that the the sampleIDs match between the metdata and otu table and that the dimensions are the same

zhouhj1994 commented 9 months ago

I am not 100 percent sure yet..It might be some issue with the rownames of the otu table. Can you check it? In addition, you could try some small subset of your data to see if the code work.