NanoStringNorm 1.1.12 2012-12-01
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BUG FIXES

* 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
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MINOR FEATURES

* 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

* 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
* Fixed volcano plot label to show log2 Fold-Change if log taken
* Fixed volcano plot y-axis break.  the xlim was not getting set properly
* 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
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MINOR FEATURES

* 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`
* Added NanoStringNorm argument `is.log`.  This switches a number of error checks i.e. no error if negative values and also changes the calculation of the geometric mean.  The purpose is to allow PCR type data to be process i.e. TLDA and OpenArray
* Added trycatch to norm.comp which returns NA if a methods fails i.e. no HK genes
* Added rescale function to Plot.NanoStringNorm in order to bound the size of points the volcano plots
* Added argument to choose sample column names from header rows.
* 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

* 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
* Fixed read.xls.RCC parsing of rows with missing values 
* Fixed missing Lane.ID in header when using reas.xls.RCC
* Added check for problem probe correction input
* Added tryCatch around mixed model ICC calculations in norm.comp i.e. HK genes reduced to zero.
* Added tryCatch around CV calculations in norm.cmop
* Fixed plotting erros for small datasets below 12 samples

