Version 4.5.0

Olink Analyze 4.5.0

Minor Changes

• Added section to LOD vignette about how to handle LOD in bridged data (#656, @KangD-dev)
• Support for NPX files from NPX Map 2.0 was added to read_NPX (#660, @kathy-nevola)
• Continuous color scale was added to PCA for graphing Olink Sample Index (OSI) continuous columns (#659, @amrita-kar)
• Function for formatting bridged data was updated to work with other types of normalization (#643, @dtopouza, #644, @klevdiamanti)

Bug Fixes

• olink_ordinalRegression changed from type = 3 to type = "marginal" to work with newest version of ordinal package (#657, @kathy-nevola)
• Regex fixed for DarID detection in olink_lod and read_NPX (#658, @kathy-nevola)

Version 4.4.0

Minor Changes

• Added support for bridging Olink Explore HT and Olink Reveal (#645, #636, #639, @boxizhang, @amrita-kar, @kathy-nevola, @dtopouza, @klev-diamanti)
• Add warning message for specific DarID-SW export combinations that require re-export (#635, @kathy-nevola)
• Added instructions for how to add LOD data to cross product bridging (#642, @KangD-dev)

Bug Fixes

• Fix wording of bridgeable assays in cross-product bridging tutorial (#632, #630, @kathy-nevola)
• Fixed warning message in case of duplicate samples so that samples with control assays did not count as duplicated samples (#634, @amrita-kar)
• QS Normalization will now exclude bridge samples with NA with warning, preventing error (#640, @klev-diamanti)

Version 4.3.2

Olink Analyze 4.3.2

Bug Fixes

• Tests for olink_wilcox() are now arranged by Assay name to handle ties (#616, @boxizhang)
• The extrafont package has been removed as a dependency as it is archived on CRAN (#619, @klevdiamanti)
• Regex in olink_lmer() has been improved to better capture the warning message (#618, @klevdiamanti)
• Handling for when AssayQC is not present in both data sets for normalization (#620, @klevdiamanti)

Version 4.3.1

Bug Fixes

• olink_lod() call to checkNPX() now correctly uses data instead of df, allowing the function to run without error (#579, @klevdiamanti)
• broken link in bridging tutorial has been fixed (#597, @amrita-kar)
• minor edits have been made to the bridging tutorial and olink_bridgeselector() to clarify how to set sampleMissingFreq argument for different products and biological contexts (#597, @amrita-kar, #596, @kathy-nevola)
• minor edits have been made to the bridging tutorial to clarify that Ct and count data is not normalized during bridging and to define a batch (#597, @amrita-kar)

Version 4.3.0

Minor Changes

• Recommended Olink Reveal bridge sample numbers have been added to the bridging tutorial (#523, @kathy-nevola)
• Missing meta-data in parquet files now result in a warning instead of an error (#540, @OlaCaster)
• Pathway enrichment updated to support msigdbr v10.0 (#542, @klevdiamanti)
• Support for PanelVersion and LODNPX was added (#551, #552, #559, @klevdiamanti, @MasoumehSheikhi)
• Support for new version of warning message when converting LME results to tidy format has been added (#565, @kathy-nevola)
• Improvements made to user interface for olink_bridgeability_plot() (#525, #522, @klevdiamanti)

Bug Fixes

• Fixed bug causing missing significance stars in olink_boxplot (#536, @boxizhang)
• Files with multiple quantification files will now select the quantification method to use (#563, @kristynchin-olink, @amrita-kar)
• OlinkIDs with multiple UniProt IDs across different panel versions will now be harmonized to one UniProt ID to allow for assays to be analyzed together (#564, @kathy-nevola)

Version 4.2.0

Olink Analyze 4.2.0

Minor Changes

• Cross-product bridging is now supported for bridging Olink Explore 3072 to Olink Reveal (#509, @kathy-nevola)
• Standard data exports from NPX Signature 2.0 are now supported (#511, @KangD-dev)
• Kang Dong and Stephen Pollo have been added as authors (#514, @kathy-nevola)
• MaxLOD will be recalculated after bridging to reflect the MaxLOD across all projects (#505, @klevdiamanti)

Bug Fixes

• A warning message will be displayed when fewer than the recommended number of bridging samples are used in cross product bridging (#507, @klevdiamanti)
• If count data is not provided in cross-product bridging, an error message will occur (#510, @kristynchin-olink)
• For cross-product bridging, if the sample type and assay warning columns do not have the same column naming (ex: SampleType and Sample_Type), both columns will be included in the output. (#515, @spollo-olprot, @MasoumehSheikh)

Version 4.1.2

What's Changed

• update unit test to remove compression by @kathy-nevola in #502

Full Changelog: v4.1.1...v4.1.2

Version 4.1.1

Olink Analyze 4.1.1

Minor Changes

• Images were decreased in dimension to meet CRAN Size requirements (#500, @kathy-nevola)

Bug Fixes

• Dataframe name was corrected in Olink Explore 3072 to Olink Explore HT bridging tutorial Downstream Analysis section. (#500, @kathy-nevola)

Version 4.1.0

Minor Changes

• Functionality has been added to read_NPX, olink_lod, and olink_plate_randomizer to support additional data types (#487, @kathy-nevola)
• A new function has been added to visualize the criteria used to establish the recommended bridging method for an assay in cross-product bridging (#468, @amrita-kar)
• A new function has been added to simplify data wrangling on bridged data after cross-product bridging (#472, @dtopouza)
• The tutorial on Olink Explore 3072 to Explore HT bridging has been updated to reflect the new functions (#473, @kristynchin-olink)
• Documentation for plate randomization when keeping samples from the same studies together has been improved in function documentation and the Plate Randomization tutorial (#483, @kathy-nevola)
• Contact us and legal disclaimer information has been updated and added to all tutorials (#490, @kathy-nevola)
• A Research Use Only (RUO) message is now printed when reading parquet files (#487, @kathy-nevola)
• References to NPX Explore have been generalized to Olink Software in tutorials (#490, @kathy-nevola)
• The overview tutorial has been updated and streamlined (#473, @kristynchin-olink)

Bug Fixes

• Assay CTRL is no longer characterized as a control assay (#484, @dtopouza)
• An error that had previously limited Explore HT to Explore HT bridging has been resolved (#491, @klevdiamanti)
• The minimum number of bridge samples for QS normalization has been corrected to 40 samples.
• The Block column is now transformed into a character value to ensure consistency across products.
• An error that had previously impacted paired Wilcoxon tests has been resolved. (#485, @boxizhang)

Version 4.0.2

Bug Fixes

• Product is now identified by column name for cross-product normalization, rather than OlinkIDs. This allows for non-overlapping assays to be present in input files. (#469, @kathy-nevola)
• Added many-to-many mapping in joining Explore HT data to the mapping file to support correlation assays (#469, @kathy-nevola)
• Corrected spelling in error message. (#469, @kathy-nevola)
• Fixed typo in NotBridgeable category name in tutorial (#471, @dtopouza)