NEWS

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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

• Submission to Bioc