Installation | 1 Example dataset | 1 Introduction | 2 Loading and Normalization of the data | 2.1 Load the raw data file and check its content. | 2.2 Normalize Dataset | 3 LOB/LOD definitions | 3.1 Assay characterization procedure | 3.2 LOB/LOD definitions | 4 Estimation of the LOB/LOD for dataset | 4.1 LOB/LOD estimation for a non-linear peptide | 4.2 LOB/LOD estimation for a linear peptide | 4.3 LOB/LOD linear estimation for a non-linear peptide | 4.4 LOB/LOD linear estimation for a linear peptide | REFERENCES
Package: MSstatsLOBD 1.21.0
Devon Kohler
MSstatsLOBD: Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) <doi:10.1074/mcp.RA117.000322>.
Authors:
MSstatsLOBD_1.21.0.tar.gz
MSstatsLOBD_1.21.0.zip(r-4.7)MSstatsLOBD_1.21.0.zip(r-4.6)MSstatsLOBD_1.21.0.zip(r-4.5)
MSstatsLOBD_1.21.0.tgz(r-4.6-any)MSstatsLOBD_1.21.0.tgz(r-4.5-any)
MSstatsLOBD_1.21.0.tar.gz(r-4.7-any)MSstatsLOBD_1.21.0.tar.gz(r-4.6-any)
MSstatsLOBD_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MSstatsLOBD/json (API)
| # Install 'MSstatsLOBD' in R: |
| install.packages('MSstatsLOBD', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vitek-lab/msstatslodq/issues
Datasets:
- raw_data - Example of dataset that contains spike in data for 43 distinct peptides.
- spikeindata - Example of normalized datasets from raw_data,
On BioConductor:MSstatsLOBD-1.21.0(bioc 3.24)MSstatsLOBD-1.20.0(bioc 3.23)
immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolmass-spectrometry
Last updated from:7c554880e0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 159 | ||
| linux-devel-x86_64 | NOTE | 165 | ||
| source / vignettes | OK | 197 | ||
| linux-release-x86_64 | NOTE | 156 | ||
| macos-release-arm64 | NOTE | 96 | ||
| macos-oldrel-arm64 | NOTE | 106 | ||
| windows-devel | NOTE | 89 | ||
| windows-release | NOTE | 92 | ||
| windows-oldrel | NOTE | 90 | ||
| wasm-release | OK | 110 |
Exports:linear_quantlimnonlinear_quantlimplot_quantlim
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecycleminpack.lmR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculation of the LOB and LOD with a linear fit | linear_quantlim |
| Calculation of the LOB and LOD with a nonlinear fit | nonlinear_quantlim |
| Plot results of nonlinear_quantlim() and linear_quantlim() | plot_quantlim |
| Example of dataset that contains spike in data for 43 distinct peptides. | raw_data |
| Example of normalized datasets from raw_data, | spikeindata |
