A dataset containing quantification of peptides using Progenesis. True
positives peptides spiked-in from the Universal Proteomics Standard Set 1
(UPS1) at three different concentrations and true negatives from
Chlamydomonas reinhardtii with the same concentration in all samples.
You can find true positives with <code>stringr::str_detect(ups$identifier, 'UPS')</code>. For details see berg2019evaluation;textualbaldur and
if you use this dataset please cite the same paper.

datasets

Statistical decision in proteomics data using a hierarchical
Bayesian model. There are two regression models for describing the
mean-variance trend, a gamma regression or a latent gamma mixture
regression. The regression model is then used as an Empirical Bayes
estimator for the prior on the variance in a peptide. Further, it assumes
that each measurement has an uncertainty (increased variance) associated
with it that is also inferred. Finally, it tries to estimate the posterior
distribution (by Hamiltonian Monte Carlo) for the differences in means for
each peptide in the data. Once the posterior is inferred, it integrates the
tails to estimate the probability of error from which a statistical decision
can be made.
See Berg and Popescu for details (<doi:10.1016/j.mcpro.2023.100658>).

Philip Berg

baldur

Bayesian Hierarchical Modeling for Label-Free Proteomics

ups function

A data frame with 10599 rows and 13 variables:<dl>
<dt>identifier</dt>
<dd>id column for features, true positives contains UPS and
true negatives contains Cre</dd><dt>fmol25_1,fmol25_2,fmol25_3,fmol25_4</dt>
<dd>Technical replicates
with true positives spiked-in from 25 fmol UPS1 peptides</dd><dt>fmol50_1,fmol50_2,fmol50_3,fmol50_4</dt>
<dd>Technical replicate with true positives
spiked-in from 50 fmol UPS1 peptides</dd><dt>fmol100_1,fmol100_2,fmol100_3,fmol100_4</dt>
<dd>Technical replicate with true positives
spiked-in from 100 fmol
UPS1 peptides</dd>
</dl>

Format

Spiked-in data set of peptides — ups

A data frame with 10599 rows and 13 variables:<dl>
<dt>identifier</dt>
<dd>id column for features, true positives contains UPS and
true negatives contains Cre</dd>

<dt>fmol25_1,fmol25_2,fmol25_3,fmol25_4</dt>
<dd>Technical replicates
with true positives spiked-in from 25 fmol UPS1 peptides</dd>

<dt>fmol50_1,fmol50_2,fmol50_3,fmol50_4</dt>
<dd>Technical replicate with true positives
spiked-in from 50 fmol UPS1 peptides</dd>

<dt>fmol100_1,fmol100_2,fmol100_3,fmol100_4</dt>
<dd>Technical replicate with true positives
spiked-in from 100 fmol
UPS1 peptides</dd>


</dl>

ups: Spiked-in data set of peptides

Description

Usage

Arguments

Format

References