Analysis of quantification error: "Aggregation function missing: defaulting to length"

[daniswan]

This is for a DIA experiment. Data was exported from Spectronaut in MSstats format. artMSQuantification ran successfully, but generated an error on artmsAnalysisQuantifications step.

Code executed

library(artMS) artmsQuantification("config.yaml", verbose=TRUE) artmsAnalysisQuantifications("results.txt", "results_ModelQC.txt", "MOUSE", output_dir = "CK5", enrich = TRUE, l2fc_thres = 1.0, choosePvalue = c("adjpvalue"), isBackground = "nobackground", isPtm = "global", mnbr = 3, isFluomics = FALSE, pathogen = "nopathogen", plotPvaluesLog2fcDist = TRUE, plotAbundanceStats = TRUE, plotReproAbundance = TRUE, plotCorrConditions = TRUE, plotCorrQuant = TRUE, plotPCAabundance = TRUE, plotFinalDistributions = TRUE, plotPropImputation = TRUE, plotHeatmapsChanges = TRUE, plotTotalQuant = TRUE, plotClusteringAnalysis = TRUE, verbose = TRUE)

error message

> artmsAnalysisQuantifications("results.txt", "results_ModelQC.txt", "MOUSE",
+                              output_dir = "CK5", enrich = TRUE, l2fc_thres = 1.0,
+                              choosePvalue = c("adjpvalue"),
+                              isBackground = "nobackground", isPtm = "global", mnbr = 3,
+                              isFluomics = FALSE, pathogen = "nopathogen",
+                              plotPvaluesLog2fcDist = TRUE, plotAbundanceStats = TRUE,
+                              plotReproAbundance = TRUE, plotCorrConditions = TRUE,
+                              plotCorrQuant = TRUE, plotPCAabundance = TRUE,
+                              plotFinalDistributions = TRUE, plotPropImputation = TRUE,
+                              plotHeatmapsChanges = TRUE, plotTotalQuant = TRUE,
+                              plotClusteringAnalysis = TRUE, verbose = TRUE)
---------------------------------------------
artMS: ANALYSIS OF QUANTIFICATIONS
---------------------------------------------
--- No Pathogen extra in these samples
>> LOADING modelqc FILE (ABUNDANCE) 
--- Total number of genes/proteins: 5169 
>> LOADING QUANTIFICATIONS (-results.txt from MSstats) 
>> IMPUTING MISSING VALUES 
--- Number of +/- INF values: 2030 
Aggregation function missing: defaulting to length
Error in vapply(indices, fun, .default) : values must be length 272297,
 but FUN(X[[1]]) result is length 1

[biodavidjm]

The problem is that the biological replicates names don't follow the artMS naming rules, i.e., Condition_name-Biological_replicate_number