I am starting to use the DEP package for analysis of differentially enriched proteins, and so far I am quite happy with it. The vignette is quite good and all the functions worked without issues.

I am however confused about the meaning of the columns in the output results generated by get_df_wide and get_df_long:

# Generate a wide data.frame
df_wide <- get_df_wide(dep)
colnames(df_wide)
 [1] "name"                     "Ubi4_1"                  
 [3] "Ubi4_2"                   "Ubi4_3"                  
 [5] "Ubi6_1"                   "Ubi6_2"                  
 [7] "Ubi6_3"                   "Ctrl_1"                  
 [9] "Ctrl_2"                   "Ctrl_3"                  
[11] "Ubi1_1"                   "Ubi1_2"                  
[13] "Ubi1_3"                   "Protein.IDs"             
[15] "Majority.protein.IDs"     "Protein.names"           
[17] "Gene.names"               "Fasta.headers"           
[19] "Peptides"                 "Razor...unique.peptides" 
[21] "Unique.peptides"          "Only.identified.by.site" 
[23] "Reverse"                  "Potential.contaminant"   
[25] "ID"                       "imputed"                 
[27] "num_NAs"                  "Ubi1_vs_Ctrl_CI.L"       
[29] "Ubi1_vs_Ctrl_CI.R"        "Ubi1_vs_Ctrl_diff"       
[31] "Ubi1_vs_Ctrl_p.adj"       "Ubi1_vs_Ctrl_p.val"      
[33] "Ubi4_vs_Ctrl_CI.L"        "Ubi4_vs_Ctrl_CI.R"       
[35] "Ubi4_vs_Ctrl_diff"        "Ubi4_vs_Ctrl_p.adj"      
[37] "Ubi4_vs_Ctrl_p.val"       "Ubi6_vs_Ctrl_CI.L"       
[39] "Ubi6_vs_Ctrl_CI.R"        "Ubi6_vs_Ctrl_diff"       
[41] "Ubi6_vs_Ctrl_p.adj"       "Ubi6_vs_Ctrl_p.val"      
[43] "Ubi1_vs_Ctrl_significant" "Ubi4_vs_Ctrl_significant"
[45] "Ubi6_vs_Ctrl_significant" "significant"  

# Generate a long data.frame
df_long <- get_df_long(dep)
colnames(df_long)

[1] "label"                    "condition"               
 [3] "replicate"                "name"                    
 [5] "intensity"                "Protein.IDs"             
 [7] "Majority.protein.IDs"     "Protein.names"           
 [9] "Gene.names"               "Fasta.headers"           
[11] "Peptides"                 "Razor...unique.peptides" 
[13] "Unique.peptides"          "Only.identified.by.site" 
[15] "Reverse"                  "Potential.contaminant"   
[17] "ID"                       "imputed"                 
[19] "num_NAs"                  "Ubi1_vs_Ctrl_CI.L"       
[21] "Ubi1_vs_Ctrl_CI.R"        "Ubi1_vs_Ctrl_diff"       
[23] "Ubi1_vs_Ctrl_p.adj"       "Ubi1_vs_Ctrl_p.val"      
[25] "Ubi4_vs_Ctrl_CI.L"        "Ubi4_vs_Ctrl_CI.R"       
[27] "Ubi4_vs_Ctrl_diff"        "Ubi4_vs_Ctrl_p.adj"      
[29] "Ubi4_vs_Ctrl_p.val"       "Ubi6_vs_Ctrl_CI.L"       
[31] "Ubi6_vs_Ctrl_CI.R"        "Ubi6_vs_Ctrl_diff"       
[33] "Ubi6_vs_Ctrl_p.adj"       "Ubi6_vs_Ctrl_p.val"      
[35] "Ubi1_vs_Ctrl_significant" "Ubi4_vs_Ctrl_significant"
[37] "Ubi6_vs_Ctrl_significant" "significant" 

Specifically what is the difference between, for example, "Ubi4_vs_Ctrl_CI.L" and `"Ubi4vsCtrl_CI.R". It might be something obvious but I am new to proteomics analysis, so could anyone elucidate me?

Session info:

Daar António,

CI.L and CI.R depict the confidence interval of the logFC. These values are generated using limma. In your example, this would be the confidence interval for the logFC of Ubi4vsCtrl. Please have a look at this other question for detailed answers on the interpretation of confidence interval values for logFC.

Best, Arne

deleted entry: double entry