yeast {baldur}

R Documentation

Spiked-in data set of reversibly oxidized cysteines

Description

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 stringr::str_detect(yeast$identifier, 'YEAST'). For details see Berg et al. (2019) and if you use this dataset please cite the same paper.

Usage

yeast

Format

A data frame with 2235 rows and 7 variables:

identifier

id column for features, true positives contains YEAST and true negatives contains Cre

ng50_1,ng50_2,ng50_3

Biological replicates with true positives spiked-in from 50 ng yeast cells

ng100_1,ng100_2,ng100_3

Biological replicates with true positives spiked-in from 100 ng yeast cells

Source

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2619-6

References

Philip Berg, Evan W McConnell, Leslie M Hicks, Sorina C Popescu, George V Popescu (2019). “Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics.” BMC bioinformatics, 20(2), 7–16.

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