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Merge pull request #8 from uclahs-cds/danknight-news-md
Changelog Markdown format
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‎NEWS ‎NEWS.md

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NanoStringNorm 3.0.0 2025-01-15
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# NanoStringNorm 3.0.0 (2025-01-15)
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REMOVED
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* Removed Excel .xls support due to broken CRAN dependency
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## Removed
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* Removed Excel `.xls` support due to broken CRAN dependency
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ADDED
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## Added
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* Added CSV support for nCounter Excel files. Excel files must be converted externally.
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NanoStringNorm 2.0.0 2023-03-21
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## Changed
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* Update changelog to Markdown format
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REMOVED
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# NanoStringNorm 2.0.0 (2023-03-21)
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## Removed
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* Removed vsn functionality due to broken CRAN dependency
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NanoStringNorm 1.2.1 2017-12-11
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BUG
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# NanoStringNorm 1.2.1 (2017-12-11)
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## Fixed
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* Fixed unclosed file connection bug
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NanoStringNorm 1.2.0 2017-08-18
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# NanoStringNorm 1.2.0 (2017-08-18)
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## Fixed
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* fixed read.markup.RCC() error on new NanoString nCounter FLEX instrument
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NanoStringNorm 1.1.22 2017-06-30
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# NanoStringNorm 1.1.22 (2017-06-30)
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## Added
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* NanoStringNorm
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- added parameters "CodeCount.summary.target" and "SampleContent.summary.target"
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- these parameters allow users to specify expected positive control and housekeeping probe summary values, which are used during the cross-sample normalization
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- this update allows for sample-independent normalization of various CodeCount and SampleContent methods
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NanoStringNorm 1.1.17 2014-01-15
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# NanoStringNorm 1.1.17 (2014-01-15)
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## Fixed
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* fixed error using only one control gene. the matrix in the apply statement was getting changed to vector.
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NanoStringNorm v1.1.16 2013-09-01
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# NanoStringNorm v1.1.16 (2013-09-01)
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## Changed
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* lme4
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-lme4 doesn't work on some platforms
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-NSN "suggests" lme4 but errored out if it was missing due to examples
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-solution was add if(require(pkg)) in examples
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-this was done for all suggests packages
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* lme4 doesn't work on some platforms
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* NSN "suggests" lme4 but errored out if it was missing due to examples
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* solution was add if(require(pkg)) in examples
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* this was done for all suggests packages
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* Runit
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if(require(RUnit)) was added to NanoStringNorm.unitTests.R. Runit was recommended by BR to be a suggests and not a depends.
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- package needs to be able to run/test with and without suggest packages
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* if(require(RUnit)) was added to NanoStringNorm.unitTests.R. Runit was recommended by BR to be a suggests and not a depends.
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* package needs to be able to run/test with and without suggest packages
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## Fixed
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* Rd line length. R-devel fails on example/usage length of 90.
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* ::: dropped in code due to check warning
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NanoStringNorm 1.1.15 2014-01-15
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# NanoStringNorm 1.1.15 (2014-01-15)
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## Fixed
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* R check compatablility
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- reduced size of high resolution bitmaps used in vignette (100kb saved!)
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- changed Nanostring to NanoString in text (seriously!)
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- made googleVis example conditional depending on installation. the package is under "suggests"
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* reduced size of high resolution bitmaps used in vignette (100kb saved!)
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* changed Nanostring to NanoString in text (seriously!)
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* made googleVis example conditional depending on installation. the package is under "suggests"
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* bug when negative control removes signal from all samples
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NanoStringNorm 1.1.14 2013-04-04
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BUG FIXES
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# NanoStringNorm 1.1.14 (2013-04-04)
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## Fixed
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* sample.content.norm. added some error handling for cases where rna.content was estimated to be zero, resulting in normalization factors that were infinity and errors in norm.comp
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NanoStringNorm 1.1.12 2012-12-01
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BUG FIXES
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# NanoStringNorm 1.1.12 (2012-12-01)
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## Fixed
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* read.xls.RCC. more informative error messages and allowed id instead of sample.id in header
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* Plot.NanoStringNorm.gvis. set default browser if not set.
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NanoStringNorm 1.1.11 2012-10-01
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MINOR FEATURES
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# NanoStringNorm 1.1.11 (2012-10-01)
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## Added
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* added parameter "guess.cartridges" in NanoStringNorm function. Cartridge estimates can be estimated from sample order and used in batch effect estimates
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* in Plot.NanoStringNorm the control types have different symbols
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* added some text to better describe the figures. also replaced the png with pdf for better resolution
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* made it so you can add manual and auto labels at the same time
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* added options label.n to specify the number of outliers to plot and label.as.legend to allow the labels to be written as a legend to avoid messy overlaps
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* output FDR qvalues
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BUG FIXES
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## Fixed
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* Plot.NanoStringNorm had a missing curly brace and forgotten browser statement
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* Shifted labels on positive.control plot to avoid overlap if long
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* Added regex for positive control names in cv plot, probe.correction function and norm.comp. sometimes the positive controls are named differently causing them to be missed during calculations
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* Fixed norm.factor plot positions when only one plot
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* changed low.cv.geo.mean method to better find low cv genes
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NanoStringNorm 1.1.10 2012-09-01
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MINOR FEATURES
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# NanoStringNorm 1.1.10 (2012-09-01)
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## Added
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* Added colour argument `col` in Plot.NanoStringNorm to change default plotting colours
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* Added function read.markup.RCC to process single sample markup RCC files
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* Changed NanoStringNorm log argument to `take.log`
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* Added argument `icc.method` in norm.comp to choose between anova (fast) and mixed (more appropriate)
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* Changed default sample name in read.xls.rcc to file.name
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BUG FIXES
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## Fixed
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* Added check in NanoStringNorm to check if input is a matrix, list, or data.frame
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* Added check for `Code.Class` colum in norm.comp. The col is referenced but the data is not exhaustively checked. The check was also added to the read.markup.RCC function
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* Added check for problem input in read.xls.RCC

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