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IngallsLabUW / Ingalls_Standards

A repository containing the Ingalls Lab standards list, available for download.
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Absolute file paths broken for manual RTs #30

Open wkumler opened 2 years ago

wkumler commented 2 years ago

Currently our extract_DDA script is looking for Skyline output files named "HILICpos_StandardMixes_All-CEs.csv" but at some point they were renamed to "HILICpos_All-CEs_NewStdMixes_5x.csv" (I think) and the script never got updated. I assume it's safe to just rename those files but wanted to note it here because currently the extract_DDA script is broken because of it.

wkumler commented 2 years ago

Existing code:

## Grab manual standard retention times
compound.data <- read.csv("data_raw/HILICpos_StandardMixes_All-CEs.csv") %>%
  rbind(read.csv("data_raw/HILICneg_StandardMixes_All-CEs.csv")) %>%
  select(compound_name="Precursor.Ion.Name",
         rt="Retention.Time",
         filename="Replicate.Name",
         mz="Precursor.Mz") %>% 
  mutate(rt=as.numeric(rt)) %>%
  mutate(filename=paste0(filename, ".mzML")) %>%
  filter(!is.na(rt))

Files in WD:

210420_Std_4uMStdsMix1InH2O_neg1.mzML
210420_Std_4uMStdsMix1InH2O_neg2.mzML
210420_Std_4uMStdsMix1InH2O_neg3.mzML
210420_Std_4uMStdsMix1InH2O_neg4.mzML
210420_Std_4uMStdsMix1InH2O_neg5.mzML
210420_Std_4uMStdsMix1InH2O_pos1.mzML
210420_Std_4uMStdsMix1InH2O_pos2.mzML
210420_Std_4uMStdsMix1InH2O_pos3.mzML
210420_Std_4uMStdsMix1InH2O_pos4.mzML
210420_Std_4uMStdsMix1InH2O_pos5.mzML
210420_Std_4uMStdsMix2InH2O_neg1.mzML
210420_Std_4uMStdsMix2InH2O_neg2.mzML
210420_Std_4uMStdsMix2InH2O_neg3.mzML
210420_Std_4uMStdsMix2InH2O_neg4.mzML
210420_Std_4uMStdsMix2InH2O_neg5.mzML
210420_Std_4uMStdsMix2InH2O_pos1.mzML
210420_Std_4uMStdsMix2InH2O_pos2.mzML
210420_Std_4uMStdsMix2InH2O_pos3.mzML
210420_Std_4uMStdsMix2InH2O_pos4.mzML
210420_Std_4uMStdsMix2InH2O_pos5.mzML
HILICneg_All-CEs_NewStdMixes_5x.csv
HILICpos_All-CEs_NewStdMixes_5x.csv
R-Lionheart commented 2 years ago

Yeah I seem to recall that we left in hard-coded stuff because of the weird connection to Google Drive. Did you end up changing the name in the code?

wkumler commented 2 years ago

I think I did this with my own copy but didn't push it anywhere. Maybe @LTCarlson remembers making this change and can confirm that these are the same files and that this is an easy fix?

LTCarlson commented 2 years ago

Yes, I believe these are the same files so I think you can just change the name if that is easiest.

R-Lionheart commented 2 years ago

I am going to leave this issue open for now.

When we know more about how UW is going to change the shared google drive, that will be a good time to update this script. I recommend looking into the "googledrive" tidyverse package if accessing the drive is still required at that time.