Custom file uploading issue about amica

[tbaccata]

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