yeast

A dataset containing quantification of reversibly oxidized cysteines using
Progenesis. True positives cysteines spiked-in from yeast at two different
concentrations and true negatives from Chlamydomonas reinhardtii with
the same concentration in all samples. To identify true positives one can use
<code>stringr::str_detect(yeast$identifier, 'YEAST')</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

yeast function

A data frame with 2235 rows and 7 variables:<dl>
<dt>identifier</dt>
<dd>id column for features, true positives contains YEAST and
true negatives contains Cre</dd><dt>ng50_1,ng50_2,ng50_3</dt>
<dd>Biological replicates with
true positives spiked-in from 50 ng yeast cells</dd><dt>ng100_1,ng100_2,ng100_3</dt>
<dd>Biological replicates with
true positives spiked-in from 100 ng yeast cells</dd>
</dl>

Format

Spiked-in data set of reversibly oxidized cysteines — yeast

A data frame with 2235 rows and 7 variables:<dl>
<dt>identifier</dt>
<dd>id column for features, true positives contains YEAST and
true negatives contains Cre</dd>

<dt>ng50_1,ng50_2,ng50_3</dt>
<dd>Biological replicates with
true positives spiked-in from 50 ng yeast cells</dd>

<dt>ng100_1,ng100_2,ng100_3</dt>
<dd>Biological replicates with
true positives spiked-in from 100 ng yeast cells</dd>


</dl>

yeast: Spiked-in data set of reversibly oxidized cysteines

Description

Usage

Arguments

Format

References