Error with groupComparisonLiP function

[jazzminda]

Hi MSstatsLiP-Team,

I have encountered an error when I use your package to build the adjusted model using the LiP and Trp datasets from the Spectronaut analysis with the groupComparisonLiP function.

The error arises with this line of code inside the function (in the MSstatsGroupComparisonOutput function):

list(ComparisonResult = as.data.frame(comparisons)[, cols], ModelQC = as.data.frame(qc), 
    FittedModel = fitted_models)

with the following error:

Error in [.data.frame(as.data.frame(comparisons), , cols) :
undefined columns selected

Apparently, the comparisons dataframe for the protein adjustment contains less variables (8) than it should.
Since this error doesn't arise when I use the data from your publication (Malinovska et al., 2023), I assume it must be something with my Trp dataset input which causes the error but I can't find what it is.

Do you have a tip for me what I would need to change in my data input?
I am using the LiP-MS analysis for a far less complex set-up (only three proteins in different combinations) than in your dataset. Might that be a problem?

Thank you in advance,
Jasmin

[devonjkohler]

Hi Jasmin,

I don't think the less complex set up should be causing any problems. Would you be able to attach a small subset of your data to this issue so that I can diagnose the problem?

Best,
Devon

[jazzminda]

Hi Devon,

of course, I attached two files, one for the Proteinase K and one for the trypsin only dataset.

I already tried different analysis settings, databases and compared my dataframes to your published ones to find the difference that creates the problem but unfortunately I haven't been successful.

Therefore, it would be really great if you were able to help me!

Thank you in advance!
Jasmin

JJ_Trp_specific_Report_excerpt.csv
JJ_ProtK_unspecific_Report_excerpt.csv

[jazzminda]

Hi Devon,

I was wondering if you already had time to look into this issue and maybe give me an update or a hint for it?

Best,
Jasmin