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Changelog Markdown format #8

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Jan 17, 2025
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Changelog Markdown format #8

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7e543b1
Update NEWS to Markdown format
dan-knight Jan 11, 2025
f864693
Update changelog
dan-knight Jan 11, 2025
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Merge branch 'main' of github.com:uclahs-cds/public-R-NanoStringNorm …
dan-knight Jan 17, 2025
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100 changes: 48 additions & 52 deletions NEWS → NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,99 +1,98 @@
NanoStringNorm 3.0.0 2025-01-15
----------------------------------------------------------------
# NanoStringNorm 3.0.0 (2025-01-15)

REMOVED
* Removed Excel .xls support due to broken CRAN dependency
## Removed
* Removed Excel `.xls` support due to broken CRAN dependency

ADDED
## Added
* Added CSV support for nCounter Excel files. Excel files must be converted externally.

NanoStringNorm 2.0.0 2023-03-21
----------------------------------------------------------------
## Changed
* Update changelog to Markdown format

REMOVED

# NanoStringNorm 2.0.0 (2023-03-21)

## Removed
* Removed vsn functionality due to broken CRAN dependency

NanoStringNorm 1.2.1 2017-12-11
----------------------------------------------------------------

BUG
# NanoStringNorm 1.2.1 (2017-12-11)

## Fixed
* Fixed unclosed file connection bug

NanoStringNorm 1.2.0 2017-08-18
----------------------------------------------------------------

# NanoStringNorm 1.2.0 (2017-08-18)

## Fixed
* fixed read.markup.RCC() error on new NanoString nCounter FLEX instrument

NanoStringNorm 1.1.22 2017-06-30
----------------------------------------------------------------

# NanoStringNorm 1.1.22 (2017-06-30)

## Added
* NanoStringNorm
- added parameters "CodeCount.summary.target" and "SampleContent.summary.target"
- these parameters allow users to specify expected positive control and housekeeping probe summary values, which are used during the cross-sample normalization
- this update allows for sample-independent normalization of various CodeCount and SampleContent methods

NanoStringNorm 1.1.17 2014-01-15
----------------------------------------------------------------

# NanoStringNorm 1.1.17 (2014-01-15)

## Fixed
* fixed error using only one control gene. the matrix in the apply statement was getting changed to vector.

NanoStringNorm v1.1.16 2013-09-01
----------------------------------------------------------------

# NanoStringNorm v1.1.16 (2013-09-01)

## Changed
* lme4
-lme4 doesn't work on some platforms
-NSN "suggests" lme4 but errored out if it was missing due to examples
-solution was add if(require(pkg)) in examples
-this was done for all suggests packages

* lme4 doesn't work on some platforms
* NSN "suggests" lme4 but errored out if it was missing due to examples
* solution was add if(require(pkg)) in examples
* this was done for all suggests packages
* Runit
if(require(RUnit)) was added to NanoStringNorm.unitTests.R. Runit was recommended by BR to be a suggests and not a depends.
- package needs to be able to run/test with and without suggest packages

* if(require(RUnit)) was added to NanoStringNorm.unitTests.R. Runit was recommended by BR to be a suggests and not a depends.
* package needs to be able to run/test with and without suggest packages

## Fixed
* Rd line length. R-devel fails on example/usage length of 90.

* ::: dropped in code due to check warning


NanoStringNorm 1.1.15 2014-01-15
----------------------------------------------------------------
# NanoStringNorm 1.1.15 (2014-01-15)

## Fixed
* R check compatablility
- reduced size of high resolution bitmaps used in vignette (100kb saved!)
- changed Nanostring to NanoString in text (seriously!)
- made googleVis example conditional depending on installation. the package is under "suggests"
* reduced size of high resolution bitmaps used in vignette (100kb saved!)
* changed Nanostring to NanoString in text (seriously!)
* made googleVis example conditional depending on installation. the package is under "suggests"
* bug when negative control removes signal from all samples


NanoStringNorm 1.1.14 2013-04-04
----------------------------------------------------------------

BUG FIXES
# NanoStringNorm 1.1.14 (2013-04-04)

## Fixed
* 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

NanoStringNorm 1.1.12 2012-12-01
----------------------------------------------------------------

BUG FIXES
# NanoStringNorm 1.1.12 (2012-12-01)

## Fixed
* read.xls.RCC. more informative error messages and allowed id instead of sample.id in header
* Plot.NanoStringNorm.gvis. set default browser if not set.

NanoStringNorm 1.1.11 2012-10-01
----------------------------------------------------------------

MINOR FEATURES
# NanoStringNorm 1.1.11 (2012-10-01)

## Added
* added parameter "guess.cartridges" in NanoStringNorm function. Cartridge estimates can be estimated from sample order and used in batch effect estimates
* in Plot.NanoStringNorm the control types have different symbols
* added some text to better describe the figures. also replaced the png with pdf for better resolution
* made it so you can add manual and auto labels at the same time
* 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
* output FDR qvalues

BUG FIXES

## Fixed
* Plot.NanoStringNorm had a missing curly brace and forgotten browser statement
* Shifted labels on positive.control plot to avoid overlap if long
* 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
Expand All @@ -102,11 +101,10 @@ BUG FIXES
* Fixed norm.factor plot positions when only one plot
* changed low.cv.geo.mean method to better find low cv genes

NanoStringNorm 1.1.10 2012-09-01
----------------------------------------------------------------

MINOR FEATURES
# NanoStringNorm 1.1.10 (2012-09-01)

## Added
* Added colour argument `col` in Plot.NanoStringNorm to change default plotting colours
* Added function read.markup.RCC to process single sample markup RCC files
* Changed NanoStringNorm log argument to `take.log`
Expand All @@ -117,9 +115,7 @@ MINOR FEATURES
* Added argument `icc.method` in norm.comp to choose between anova (fast) and mixed (more appropriate)
* Changed default sample name in read.xls.rcc to file.name


BUG FIXES

## Fixed
* Added check in NanoStringNorm to check if input is a matrix, list, or data.frame
* 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
* Added check for problem input in read.xls.RCC
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