SC: 2009年8月19日阅读。米尔交付RGList或EList取决于Bg值的存在SC: 20 2009年8月在lv纠正错误。EList提供总结的时候。args EList对象添加一些S4方法处理EList或者ExpressionSet一样(v 0.1.2) SC: 1 2009年9月添加方法EList和RGList estVC (v0.1.3)添加方法RGList效用函数(参见utils.R) SC: 2009年9月11日在总结纠正错误。EList SC: 2009年9月11日添加vsn正常化选项SC: 2009年9月14日vsn G-Gb SC可能工作:2009年9月19日平均波兰现在允许不平衡(#)复制YP: 4 2009年10月向estVC添加选项。std -加权或渐近方差公式——联合均值和方差模型,或只意味着模型——删除contr.helmert(恢复contr.treatment)——输出包括ArrayEffects表达指数SC: 2009年10月10日固定的总结。R和规范化。R函数来适应新的estVC产出——“lv”内,使用列表summarize.args =(方法=“那么使用rlm”)将使用数组estVC估计的影响。SC: 2009年10月14日总结现在默认是“那么使用rlm”使用数组影响那么使用rlm计算。SC: 2009年10月16日添加选项(Atransf = c(“√”、“日志”)选择的变换阵列卡方最初只有√)。绘制方法相应地修改。SC: 2009年10月22日虫固定在阅读。米尔,跳过论点没有自动连接指针的转变。 Now use of seek (for OS where seek works) or reopening connection (Windows) would place the pointer back to the beginnig SC: 18 Nov 2009 v 0.2.4 Added option for stratified identification of lvs set, based on quantiles of reference distribution (default: median i.e. n.strata =2) SC: 20 Nov 2009 v 0.2.5 added option for parallel computation using either multicore or snow SC: 26 Nov 2009 v 0.2.5 method default changed to "joint" in estVC SC: 21 Jan 2010 v 0.2.6 maxit in gamma.glm is 20 and residuals are checked for being bigger than .Machine$double.eps ^ 0.5 instead of zero SC: 22 Jan 2010 v 0.2.7 - Allow to use affyPara for vsn computation. - Fixed bug on ArrayEffects ordering SC: 25 Jan 2010 v 0.2.8 - vsn parallel computation implemented without using affyPara in order to use "multicore". For relatively small samples using snow the way affyPara does increases the data transfer burden (we now split along cols) which make the program running slower. It might me useful for bigger sample size (how much?). Using multicore avoids data transfer to cores. SC: 26 Jan 2010 v 0.3.0 - C version for rlm and joint fit. SC: 25 Jan 2010 v 0.3.1 - Changed split to adapt to number of cores. This would affect only parallel computation SC: 02 Feb 2010 v 0.3.2 - Fixed some bugs in C code (max_iter was not set properly). - Removed splitting and in 0.3.1 as it doesn't improve computation time. - Removed parallel vsn as it must be better setup. TODO - Added option for plotting quantile line in plot.RA - Now selection on LVS probes can be done also setting an horizontal line - Now lvs accepts as argument a named vector that specify the LVS probes (selected outside) SC: 09 Feb 2010 v 0.3.3 - lvs allows to keep the LVS probe names as an attribute SC: 08 Mar 2010 v 0.3.4 - fixed bug in using level=probe SC: 22 Mar 2010 v 0.3.5 - little change in plot.RA (arg col.black and lwd=1.5 in rq line) SC: 24 Mar 2010 v 0.3.6 - Added converged and # of iterations in C code for rlm fit SuoChen: 24 May 2010 v 0.3.7 - Added man pages, examples and data SC: 25 May 2010 v 0.3.8 - Fixed man and some warnings in R CMD check SC: 04 Jun 2010 v 0.3.9 - Added a mixed VSN-smooth normalization method: normalization based on smooth-spline followed by variance stabilization without calibration (method="mixed") SC: 17 Jun 2010 v 0.3.10 - Added vignette SC: 30 Aug 2010 v 0.3.11 - Added NAMESPACE and modified "internal" functions to start with ".". Also some fix for parallel execution in Windows. SC: 30 Aug 2010 v 0.9.1 - First version for submission to Bioconductor SC: 15 Sep 2010 v 0.9.3 - First revision for submission to Bioconductor SC: 20 Sep 2010 v 0.9.4 - Second revision for submission to Bioconductor. Removed usage of . for hidden functions. Fixed vignette SC: 08 Dec 2010 v 1.1.2 - Fixed switch() in plot (utils.R) syntax (only 1 unnamed argument when the first is character) SC: 12 Apr 2014 v 1.3.4 - Fixed some warnings from R 3.1.0 - ream.mir now simply calls read.maimage from limma