I'm trying to use STAMP to analyze and visualize the results of a functional prediction made with PICRUSt2. I have 3 different result files (KO predictions, EC predictions and pathway predictions) all in tsv format and a metadata file in txt format. I tried loading the files with their original format and also tried converting the KO predictions table to biom format and then constructing a STAMP profile, but in all of these cases, when uploading the files I get the error "KeyError: It occured at line 44 of file Metadata.py".
I don't know if this error is connected to the fact that all of the p-values and Corrected p-values are equal to 1.000 in all the features and there's a note in all of the KOs saying "degenerate case: at least one group contains less than 2 samples". I made another biom file without the KOs that only appear in one sample or in none. but the p-vales are still equal to 1.000. I need to know what KOs are significant for constructing the heat map.
Hi,
I'm trying to use STAMP to analyze and visualize the results of a functional prediction made with PICRUSt2. I have 3 different result files (KO predictions, EC predictions and pathway predictions) all in tsv format and a metadata file in txt format. I tried loading the files with their original format and also tried converting the KO predictions table to biom format and then constructing a STAMP profile, but in all of these cases, when uploading the files I get the error "KeyError: It occured at line 44 of file Metadata.py".
I don't know if this error is connected to the fact that all of the p-values and Corrected p-values are equal to 1.000 in all the features and there's a note in all of the KOs saying "degenerate case: at least one group contains less than 2 samples". I made another biom file without the KOs that only appear in one sample or in none. but the p-vales are still equal to 1.000. I need to know what KOs are significant for constructing the heat map.
So any ideas why the p-values are not calculated?
Any help would be very much appreciated
I attach the original KO file, the filtered file and the mapping file ko_predictions_filtered.txt KO_predictions.txt mapping_file.txt