Error in Preprocessing Function

[LarryMe27]

Hi together,
I used this code and wanted to skip preprocessing:

library(HiTMaP)

datafile=c("Data/kidney_Lme033.imzML")
wd="D:/data/Larissa/R_proj/"


preprocess = list(force_preprocess=FALSE,
                  use_preprocessRDS=TRUE)

imaging_identification(datafile=paste0(wd,datafile),
                       trehold=0.5,
                       ppm=20,
                       Digestion_site="trypsin",
                       missedCleavages=0:1,
                       Fastadatabase="Maus_2024_05_15.fasta",
                       adducts= c("M+H"),
                       Decoy_mode = "isotope",
                       mzrange=c(800,2000),
                       parallel=12,
                       Segmentation="spatialKMeans",
                       preprocess = preprocess,
                       Region_feature_summary = TRUE,
                       score_method="SQRTP",
                       Protein_feature_summary = TRUE,
                       plot_ion_image = TRUE,
                       Peptide_feature_summary = TRUE)

I got this returned:
224 Cores detected, 4 threads will be used for computing
1 files were selected and will be used for Searching
Maus_2024_05_15.fasta was selected as database. Candidates will be generated through Proteomics mode
Found enzyme: trypsin
Found rule: ""
Found customized rule: ""
Testing fasta sequances for degestion site: (KR)|((?<=W)K(?=P))|((?<=M)R(?=P))
Generated 54910 Proteins in total. Computing exact masses...
Generating peptide formula...
Generating peptide formula with adducts: M+H
Calculating peptide mz with adducts: M+H
Candidate list has been exported.
Maus_2024_05_15.fasta was selected as database
Spectrum intensity threshold: 0.10%
mz tolerance: 20 ppm Segmentation method: spatialKMeans
Manual segmentation def file: None
Bypass spectrum generation: FALSE
Found rotation info
Loading raw image data for statistical analysis: kidney_Lme033.imzML
parsing imzML file: ‘D:\data\Larissa\R_proj\Data\kidney_Lme033.imzML’
detected 'processed' imzML
creating MSImagingExperiment
applying profile m/z-values to all spectra
using mass.range 800 to 2000
using resolution 5 ppm
binning intensity from mz 800 to 1999.9985 with relative resolution 5e-06
returning MSImagingExperiment
done.
Preparing image data for statistical analysis: kidney_Lme033.imzML
Error in if (preprocess$smoothSignal$method == "Disable") { :
argument is of length zero

Could you please help me with this?
Thanks in advance

[LarryMe27]

Short addition if I enable preprocessing I get this return: Error in matrix(0, nrow = N, ncol = k, dimnames = list(snames, paste0("C", :
length of 'dimnames' [2] not equal to array extent.

This is my code for the preprocessing: preprocess = list(force_preprocess = FALSE, use_preprocessRDS = TRUE, smoothSignal =
list(method = "enable"),peakAlign = list(tolerance = 20, units = "ppm"),
peakFilter = list(freq.min = 0.05))

[MASHUOA]

Hi, Larry,
Could you please try to use validate_preprocess_params() to check the available method for each step? it also helps you to fill in all the other missing arguments with defaults.
let me know if it helps.