ModelQC NULL in MSstatsTMT

[Sam Siljee]

Dear MSstatsTMT team,

I'm having trouble with the `groupComparisonTMT` function where the ModelQC does not seem to be saved.

I'm using the example data as such:

TMT_input <- PDtoMSstatsTMTFormat(annotation = annotation.pd, input = raw.pd)
TMT_processed <- proteinSummarization(input.pd)
TMT_compared <- groupComparisonTMT(TMT_processed, save_fitted_models = TRUE)

TMT_compared$ModelQC

NULL

Is there something I'm doing wrong here?

Thanks!

Sam

[Sam Siljee]

Session information:

R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_New Zealand.utf8  LC_CTYPE=English_New Zealand.utf8  
[3] LC_MONETARY=English_New Zealand.utf8 LC_NUMERIC=C                        
[5] LC_TIME=English_New Zealand.utf8    

time zone: Pacific/Auckland
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] lubridate_1.9.2  forcats_1.0.0    stringr_1.5.0    dplyr_1.1.2    
 [5] purrr_1.0.1      readr_2.1.4      tidyr_1.3.0      tibble_3.2.1    
 [9] ggplot2_3.4.2    tidyverse_2.0.0  MSstatsTMT_2.8.0

[Mateusz Staniak]

Hi,

this slot only exists for consistency with MSstats output and possible future outputs, it's not supposed to be filled right now.

Kind regards,

Mateusz

[Sam Siljee]

Thank you for clarifying Mateusz!

Sam