search

MonashProteomics / FragPipe-Analyst

GNU General Public License v3.0
10 stars 4 forks source link

Absence/Presence error on DIA analysis #15

Closed Hailey-Z closed 1 year ago

Hailey-Z commented 1 year ago
image
hsiaoyi0504 commented 1 year ago

hide for now, will fix it later. 287dfe5

hsiaoyi0504 commented 1 year ago

The first reason of this error is because we don't have Combined Total Peptides in the FragPipe output right now.

hsiaoyi0504 commented 1 year ago

Another reason, as described in #20, is that we currently use path as colnames. Additionally, we don't have replicate in the example DIA dataset.

hsiaoyi0504 commented 1 year ago

Fixed in 102195a. @Hailey-Z Can you check again if it works now?

Hailey-Z commented 1 year ago

Hi @hsiaoyi0504, modified it to hide the check box on DIA absence/presence page, as it seems the DIA dataset doesn't have Combined Total Peptides column, please check it here: db8eb20407cb16efb15c81b9136b2a776dd247db.

Happy if you would like to polish this phrase https://github.com/MonashProteomics/FragPipe-Analyst/blob/db8eb20407cb16efb15c81b9136b2a776dd247db/ui.R#L471

hsiaoyi0504 commented 1 year ago

@Hailey-Z It looks ok to me, but probably you should include the corresponding shinyjs::show part for LFQ, or it would become a bug if a user submits a DIA data first and then uploads another LFQ data later.

Hailey-Z commented 1 year ago

@hsiaoyi0504 Thanks Leo, added in this commit 03e6ef5973ad082e1d98afe044fde46330f4aab3.