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cant make the correct matrix

Hi what I wanted to do is have the different Wong conditions (14) along the top and then inset the log fold values underneath. I also have joined the GS(gene symbols) from both data sets. Its not working and I don't know why, please can anyone help?

library(readr)
library(dplyr)
library(readxl)

# 1. Load the Reshaped CSV (renamed)
file_path <- "C:/Users/ns01288/Documents/tarney_wong_joined_logfc_renamed.csv"

tryCatch({
  tarney_df <- read_csv(file_path)
}, error = function(e) {
  stop(paste("Error reading renamed CSV file:", e))
})

# 2. Load the Wong Excel Data
excel_path <- "C:/Users/ns01288/OneDrive - University of Surrey/data using disertation/Total_Proteome_wong_et_al_Tarney_et_al.xlsx"
tryCatch({
  wong_df <- read_excel(excel_path, sheet = "Wong_et_al_Total_Proteome")
}, error = function(e) {
  stop(paste("Error reading Wong Excel file:", e))
})

# 3. Join Based on Gene (GS)
combined_df <- tarney_df %>%
  left_join(wong_df, by = "GS", suffix = c(".tarney", ".wong"))

# 4. Replace Tarney "n/a" with Wong Data
for (col in colnames(wong_df)[-1]) { # Iterate over Wong condition columns
  combined_df$TP_Tarney_et_al_logFC_LGSOCvsTube <- ifelse(
    combined_df$TP_Tarney_et_al_logFC_LGSOCvsTube == "n/a",
    combined_df[[paste0(col, ".wong")]],
    combined_df$TP_Tarney_et_al_logFC_LGSOCvsTube
  )
}

# 5. Select the desired columns, keeping Tarney data separate, and adding Wong data as extra columns.
final_df <- combined_df %>%
  select(GS, TP_Tarney_et_al_logFC_LGSOCvsTube, colnames(wong_df)[-1])

# 6. Write to CSV
new_file_path <- "C:/Users/ns01288/Documents/tarney_wong_joined_logfc_combined_renamed.csv"

tryCatch({
  write_csv(final_df, new_file_path)
  print(paste("Combined renamed data saved to:", new_file_path))
}, error = function(e) {
  stop(paste("Error writing CSV file:", e))
})
logfc csv
• 677 views • link
updated by lieven.sterck lieven.sterck • written by Naila • Naila

This what the csv file look like

GS,TP_Tarney_et_al_logFC_LGSOCvsTube,P.Value,Condition,LogFC
TEKT4,-2.41971357329783,6.62226226973183e-23,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
CROCC,-2.66099126705531,5.49767753170685e-23,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
LRRC23,-2.2327989494761,5.1904022851442096e-23,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
MLF1,-3.22793465818543,1.74355676260876e-22,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
SAXO2,-2.58097353155963,2.4798723472614e-22,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
CCDC151,-2.03191540707386,4.591232655773119e-22,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS125,2.859113845
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS111,1.532280638
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS127,-0.309651611
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS128,0.98624338
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS131,-1.181272098
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS107,3.028579858
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS108,0.708143704
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS101,-0.071148176
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS102,3.985737209
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS124,0.854255966
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS112,-0.611766988
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS126,-0.071788177
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS129,-1.036444137
SPATA18,-3.29617575891952,4.27286292136911e-22,Wong_et_al_TP_LGS130,-1.537097187
PPIL6,-2.76725897798818,3.27818933774816e-21,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
DNAH5,-2.52604086722928,3.10253619210591e-21,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
NME9,-2.54366451539634,5.72277545273211e-21,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
DNAH10,-2.18361481080545,7.124127398613081e-21,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
DNAJB13,-2.83710896885775,1.8594797214691098e-20,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
CEP290,-1.63479465750911,3.24150063938857e-20,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
DNAL4,-2.79400938444549,3.05058907305361e-20,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
TTC25,-2.80076368835513,5.6734199770388e-20,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
DNAJB6,-3.38523506903658,6.21406234130094e-20,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
ANXA13,-3.22816722379914,9.11272863189027e-20,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
MNS1,-2.57032863700874,1.3014055533548798e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
EFHC1,-2.64734609947182,2.14949888489187e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
CCDC114,-2.45000111714511,2.64933705989881e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
CFAP77,-2.56787026946101,2.60212136947899e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
TSGA10,-2.33275051555735,2.85209789258633e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
DNAH9,-2.38882878955434,3.1745930062973895e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
TEKT3,-2.64568802738241,4.51662675613301e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
MYCBPAP,-2.31479016185772,4.5143912776122495e-19,TP_Tarney_et_al_logFC_LGSOCvsTube,n/a
• 0 views • link
updated by lieven.sterck lieven.sterck • written by Naila • Naila

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