NEWS
msqrob2 1.19
msqrob 1.19.1
- Add functions to calculate log-normalisation factors that can be used with
sweep function
- Add function msqrobCollect to collect results tables
- Add function plotVolcano to make volcanoplots for hypothesisTest tables
- Add function createPairwiseContrasts to generate contrasts for all pairwise
comparisons
- Illustrate these new functionalities in the vignettes
- New Vignettes for DIA (DIA-NN and Spectronaut)
msqrob2 1.19.2
- Update cptac vignette (fread with argument check.names = TRUE)
msqrob2 1.19.3
- Update vignettes (arguments fread check.names = TRUE and integer64 = "double")
to avoid issues with readQFeatures
- Update README to point to msqrob2book
msqrob2 1.17
msqrob 1.17.2
(nothing yet)
msqrob 1.17.1
- Fixed NEWS file
- Fixed vignette upon renaming of longFormat to longForm
msqrob 1.17.0
- New Bioconductor devel release 3.22
msqrob2 1.16
msqrob 1.16.0
- New Bioconductor stable release 3.21
msqrob2 1.15
msqrob 1.15.1
- fix: fixed fnames in cptac vignette and moved away from
msdata to
rely on MsDataHub instead
msqrob 1.15.0
- New Bioconductor devel release 3.21
msqrob2 1.14
msqrob 1.14.1
- Added more flexibility in the msqrobLM function for models with missing variables
- Fixed full rank check for models without ridge in certain cases
msqrob 1.14.0
- New Bioconductor stable release 3.20
msqrob2 1.13
msqrob 1.13.1
- Implemented msqrobAggregate() method for SummarizedExperiment objects.
msqrob 1.13.0
- New Bioconductor devel release 3.20
msqrob2 1.12
msqrob 1.12.0
- New Bioconductor stable release 3.19
msqrob 1.11.2
- Fixed issue related to levels of a ridge variable
- Fixed issue when fitting only one random effect
msqrob 1.11.1
- Fixed issues related to reference class changes in the models
- Fixed issue related to colData assay levels
- Refactored internal code
msqrob 1.6.2
- Fixed issues related to residual degrees of freedom of overparameterized models.
- Fixed issue relating to coldata variables as factors.
msqrob2 1.5.4
- Removed the full lmer model that was accidently left in the statmodel object.
msqrob2 1.5.3
- Added the option to use mixed models without ridge regression
- Added the option to use rowdata variables in the mixed models
msqrob2 1.5.1
- Fix weighted variance covariance matrix and QR decomposition in the msqrobLmer function
msqrob2 1.1.1
- Fix filtering steps in vignette: now using
QFeatures::filterFeatures()
msqrob2 0.99.6
- Update authors in Description file
msqrob2 0.99.5
- Fix standard errors on the model parameter estimates by msqrobLmer when using doQR = TRUE
msqrob2 0.99.4
- Minor update vignette. Replace eval=FALSE in one R chunk so that the code is evaluated.
msqrob2 0.99.3
- Resolved notes on signalers
- Resolved examples with lines wider than 100 characters
- Avoiding sapply and 1:...
msqrob2 0.99.2
- Added a
NEWS.md file to track changes to the package.
- Changed dependency from R (>= 4.0) to R (>= 4.1)
- Updated citation file
Changes in version 0.99.1