What are the values in the Lefse output table given for each group of samples (to the right of FDR values and to the left of LDA score) ? For example, for one row of output, I have three groups being compared:
AL, IF, and RB
The values for “Lactobacillus” are 90667.0, 384380.0, and 4194.1, respectively.
The barplot associated with this row shows Abundance on the y-axes (filtered count or log-transformed count) but these values (which correspond to those in the output table) are at least 1-2 orders of magnitude higher than any of the read abundances in the feature table (even summed across samples within a group). Is it due to the Total Sum Scaling normalization step? Any help in interpreting these values would be helpful. In the stand alone Lefse, they say the values are log values of the highest mean abundance, but that can’t be the case here.
Thank you,
Heather
Hello, the values present in the table is the result from Linear Discriminant analysis (lda function from MASS package). The values are not log transformed.
Thank you for the reply.
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