Comments (1)
Hello!
amica needs to find a common pattern for the relevant columns (e.g intensities),
assuming that columns 388 to 408 correspond to your intensitity columns, you would need to rename them to include a common pattern (e.g add an LFQIntensity
- prefix):
Protein.Group | Protein.Ids | Protein.Names | Genes | First.Protein.Description | LFQIntensity_Control_388 | LFQIntensity_Control_399 | LFQIntensity_Control_404 | LFQIntensity_KO_405 | LFQIntensity_KO_407 | LFQIntensity_KO_408 |
---|
After adding this prefix to the column names of the data and saving this file as a tab-delimited txt file, you can create your tab-delimited exp. design and contrasts txt files, and a tab-delim. specification file, that maps relevant columns in your data to amicas format (see attached files).
In your case, you need to select a protein id (this column needs to have unique entries), a gene name and the intensity prefix:
Variable | Pattern |
---|---|
proteinId | Protein.Ids |
geneName | Genes |
intensityPrefix | LFQIntensity_ |
Hope that helps!
Best,
Sebastian
contrasts.txt
design.txt
specification.txt
from amica.
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from amica.