Problem running the example

[npalacioescat]

Describe the bug Running the example described in the README with the provided example data fails.

To Reproduce Steps to reproduce the behavior:

1. Loaded the IceR with library(IceR)
2. Opened the GUI with runIceR()
3. Set up the pointers to the directories where the raw and MaxQuant data were downloaded
4. Reduced number of cores to 4 as described in the README
5. Left all other parameters to default values (see below)

Expected behavior To be able to reproduce the example without errors

Traceback

Loading required package: shiny

Listening on http://127.0.0.1:3538
[1] "2021-02-05 10:41:40 Job started"
[1] "2021-02-05 10:41:40 Preparation finished"
[1] "2021-02-05 10:41:40 Raw file conversion finished"
[1] "2021-02-05 10:41:40 Preparation of mzXMLs finished"
[1] "Read MaxQ results"
[1] "Read MaxQ results finished"
[1] "Prepare for peptide feature matching - Indexing all ions"
[1] "Train RF models for mz-corrections"
[1] "20200110_QE1_DDA_1H25_T5_E9_R1: R^2 train-set=0.95, R^2 eval-set=0.94"
[1] "2021-02-05 10:53:10 Feature alignmend finished"
[1] "Added 18798 isotope features."
[1] "2021-02-05 10:53:11 Addition of +1 isotope features finished"
Warning: Error in colnames<-: attempt to set 'colnames' on an object with less than two dimensions
  2: shiny::runApp
  1: runIceR

Log file N/A

Desktop (please complete the following information):

• OS: Windows 7 Professional SP1
• R version: 4.0.3
• ProteoWizard version: 3.0.18247.49b14bb3d
• Version or commit hash: d802b33

Additional context Parameter file:

Settings_name | Setting
-- | --
Path to raw files | F:/IceR_example/Raw_files/
Path to MaxQ results | F:/IceR_example/MaxQ_results
Path to results | F:/IceR_example/IceR_example_results
Analysis name | IceR_example
mz_window |  
RT_window |  
min_mz_window | 0.001
min_RT_window | 1
feature_mass_deviation_collapse | 0.002
only_unmodified_peptides | FALSE
align_unknown | FALSE
use_isotope_peaks | TRUE
peak_detection | TRUE
abundance_estimation_correction | TRUE
alignment_score_cut | 0.05
Quant_pVal_cut | 0.05
n_cores | 3
RT_correction | TRUE
mz_correction | TRUE
add_PMPs | FALSE
plot_peak_detection | FALSE
calc_protein_LFQ | TRUE
kde_resolution | 50
num_peaks_store | 5
MassSpec_mode | Orbitrap
use_IM_data | FALSE
Multiplicity | 1
Light_labels |  
Medium_labels |  
Heavy_labels |  

[mathiaskalxdorf]

Hi @Nic-Nic,

based on the traceback console log you reported, it looks like you only provided a single out of 4 raw files (example data set) to IceR [1] "Train RF models for mz-corrections" [1] "20200110_QE1_DDA_1H25_T5_E9_R1: R^2 train-set=0.95, R^2 eval-set=0.94" IceR reports the results of the random forest model fittings for every sample individually so here you should see 4 instead of 1 line. Furthermore, I don´t see that IceR automatically triggered raw to mzxml conversion. Did you do this manually or was it done by IceR in a first attempt? If done manually, please check that (for your example path):

• still all raw files are found in in F:/IceR_example/Raw_files/
• all corresponding mzXML files with matching names (file names have to be identical between raw and mzxml files, only file extension should be different) are found in F:/IceR_example/Raw_files/mzXML

Can you check that all raw files are available in your specified folder? Please also cosider removing the Temporary_files folder in F:/IceR_example/IceR_example_results when you start IceR the next time to enable a fresh run.

The next release of IceR will also contain some additional warning messages if certain criteria are not met.