Nesvilab / FragPipe-Analyst

An easy-to-use and interactive web application for FragPipe

https://fragpipe-analyst-doc.nesvilab.org/

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Does FragPipe-Analyst support multi-fraction runs? #10

Closed TeckYewLow closed 1 year ago

TeckYewLow commented 1 year ago

Hi,

I am playing around with a label-free DDA datasets which contains many samples and each sample is fractionated by basic C18 into many fractions. This is quite different from the example given in the tutorial where each samples comprise one LC-MS run. How can I configure the experiment annotation file to allow FragPipe-Analyst analysis?

Best,

Teck

TeckYewLow commented 1 year ago

I tried to run it on the https://fragpipe-analyst.org/ server. I got an error message, i.e.,

error in evaluating the argument 'x' in selecting a method for function 'nrow': error in evaluating the argument 'x' in selecting a method for function 'assay': duplicate 'row.names' are not allowed

hsiaoyi0504 commented 1 year ago

Duplicated as MonashProteomics/FragPipe-Analyst#79.

hsiaoyi0504 commented 1 year ago

From your result, fractions are combined into one in the combined_protein file. So you will need to only keep one row for all fractions from the same sample. I emailed the modified version to @alyssaxin already. Note that I am not sure if you do have that many replicates.