Error in the msstats_tmt.R function parse_contrasts

[kai-lawsonmcdowall]

Description of the bug

There are appears to be a bug in the msstats_tmt.R function, which is executed by the process MSSTATS_TMT module. Specifically, in the parse_contrasts function. The error which I received was:

  Error in parse_contrasts(l = l, contrast_str = contrast_str, lvls = lvls) : 
    object 'i' not found
  Execution halted

SDRF I used is attached, the original .raw files can be found at PXD018893.

PXD018893_2025-08-04.sdrf.tsv

The params file was params.json, I'm also happy to provide the fasta database file if required.

And the nextflow.log was

issue_nextflow.log

In believe the issue originates In the else block (when control_str != ""):

for (j in setdiff(1:l, control)) {
    comparison <- rep(0, l)
    comparison[i] <- -1   # <--- 'i' isnt defined here
    comparison[j] <- 1
    contrast_mat[c,] <- comparison
    rownames(contrast_mat)[c] <- paste0(lvls[i], "-", lvls[j])
    c <- c + 1
}

We only loop over j (the non-control levels).

we don't declare i in this scope, so when we call comparison[i] <- -1, it errors with:

Error in comparison[i] <- -1 : object 'i' not found

From my understanding and based on the context, i was meant to represent the control group index, which we have here

control <- which(as.character(lvls) == control_str)

So inside that loop, we should use control instead of i:

comparison[control] <- -1
comparison[j] <- 1
rownames(contrast_mat)[c] <- paste0(lvls[control], "-", lvls[j])

Command used and terminal output

nextflow run main.nf -profile docker -params-file params.json

Relevant files

No response

System information

N E X T F L O W version 25.04.2 build 5947 Local Local Docker Ubuntu 22.04

[jpfeuffer]

@kai-lawsonmcdowall Please let us know if your merged PR fixed that problem. Thanks for the contribution.