Hi
I am running direct_lfq using the default parameters and a general format input file. The input file contains the protein and ion columns as well as 11 "intensity" columns obtained from 11 files. In the output file ("protein_intensities.tsv") some protein have zero values for some files, but nonzero ion intensities in the input; I do not understand how this is possible. Unfortunately, the input file is too big to share here, but to explain my issue, I have attached a file containing an example protein. In the example file the lines (from the input) that contain the protein NP_001035879.1 are given. As you can see from the attached file, although there some zero ion intensities, the protein has a few nonzero values for each of the 11 files. Thus, I expect the protein intensities to be nonzero across all files, but the output of directlfq for this protein looks like this (again, since the output file is very large, I am sharing only this one line from the output):
NP_001035879.1|Homo.sapiens 0.0 1480749.5567460337 18001180.447549194 0.0 0.0 167160460.21720338 1634232.2042698557 0.0 0.0 0.0 0.0
In other words the protein in question has nonzero values only in 4 out of the 11 files. How is this possible? Am I missing something?
Thank you in advance for your help.
example.csv
Hi
I am running direct_lfq using the default parameters and a general format input file. The input file contains the protein and ion columns as well as 11 "intensity" columns obtained from 11 files. In the output file ("protein_intensities.tsv") some protein have zero values for some files, but nonzero ion intensities in the input; I do not understand how this is possible. Unfortunately, the input file is too big to share here, but to explain my issue, I have attached a file containing an example protein. In the example file the lines (from the input) that contain the protein NP_001035879.1 are given. As you can see from the attached file, although there some zero ion intensities, the protein has a few nonzero values for each of the 11 files. Thus, I expect the protein intensities to be nonzero across all files, but the output of directlfq for this protein looks like this (again, since the output file is very large, I am sharing only this one line from the output):
NP_001035879.1|Homo.sapiens 0.0 1480749.5567460337 18001180.447549194 0.0 0.0 167160460.21720338 1634232.2042698557 0.0 0.0 0.0 0.0
In other words the protein in question has nonzero values only in 4 out of the 11 files. How is this possible? Am I missing something?
Thank you in advance for your help.
example.csv