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tbaccata / amica

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
GNU General Public License v3.0
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Custom file uploading issue #6

Closed rajeshksoni11 closed 2 years ago

rajeshksoni11 commented 2 years ago

HI, I have t output from DIA-NN, would you able to help for correct formatting.

Protein.Group | Protein.Ids | Protein.Names | Genes | First.Protein.Description | 388 | 399 | 404 | 405 | 407 | 408 388 _Control 399_Control 404_Control 405_KO 407_KO 408_KO

Best,

tbaccata commented 2 years ago

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