test(groupComparisonPTM): Fix unit test to expect warning due to tech replicates

[tonywu1999]

Motivation and Context

This change caused this PTM unit test to fail because the change caused the MSstats code to use a linear mixed effects model with an additional random effect w.r.t. GROUP:SUBJECT pairings (via the introduction of technical replicates). This causes the model to run out of degrees of freedom for cases where number of samples is low overall, generating warnings (it's a little more complicated than number of samples but basically we lose degrees of freedom with the introduction of an additional random effect).

Changes

• Remove proteins from datasets (raw.input and summary.data) where degrees of freedom run out. Notably the 4 proteins in the PTM dataset:
  • Q9UNN5_K163
  • Q9UNS2_K179
  • Q9Y3I0_K492
  • Q9Y490_K2115

Testing

• Dry run passes
• Tests pass locally when using latest version of MSstats
  • We should push this change to MSstatsPTM before pushing MSstats to bioconductor.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules