limpa

[gksmyth]

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[bioc-issue-bot]

Hi @gksmyth

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: limpa
Version: 0.99.0
Date: 2025-01-03
Title: Linear Models for Proteomics Data
Description: Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying expression level of each peptide, and uses it to incorporate peptide missing values into protein quantification and subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma.
Authors@R: c(person("Mengbo", "Li",
  email = "[email protected]",
  role = "aut",
  comment = c(ORCID = "0000-0002-9666-5810")),
  person("Gordon", "Smyth",
  email = "[email protected]",
  role = c("cre", "aut"),
  comment = c(ORCID = "0000-0001-9221-2892")))
License: GPL (>=2)
Depends: limma
Imports: methods, stats, data.table, statmod
Suggests: knitr, BiocStyle
VignetteBuilder: knitr
biocViews: Bayesian, DataImport, DifferentialExpression, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, Regression, Software

[lshep]

I am worried about the name of the package and how close to the already existing limpca. I'll look over for other pre-review conditions in the next few days but wanted to mention this while I was thinking of it.

[gksmyth]

We could like to keep the limpa name if at all possible. The name is simple, catchy and emphasises the close relationship with the limma package. The relationship with limma is close, because limpa` starts by reading in precursor-level data from DIA-NN, Spectronaut or MaxQuant and finishes with a limma linear-model object for downstream analysis in limma. The first author, Mengbo Li, has been invited to present a workshop in Boston in a few months with the title:

Workshop Title: "Missingness-informed protein quantification and differential expression analysis powered by limma and limpa"

so you can see how the two package names go together.

I can see that limpca has only one extra letter, but I doubt there will be much confusion in practice. It's a pity that limpca wasn't called lmpca, which to me would have been more natural as well as shorter. All other Bioconductor packages with names starting with "lim" have some connection with limma.

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[bioc-issue-bot]

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