包:codelink = = = = = = = = = = = = = = = = = = = =版本1.38.0 o固定错误阅读codelink文件选项类型=“原始”或类型=“常态”。o现在readCodelinkSet()接受“路径= "作为参数,使阅读文件从一个目标目录。版本1.32.0 o只是小修小补文档。o把旧词“Bioarray”(最初用于第一Codelink平台)描述文件。版本1.30.0 o CodelinkSet类被采用为官方支持类存储Codelink数据。文档关于这个话题已得到改进,和一个新的小插图描述CodelinkSet接口(Codelink_Introduction)。老Codelink类文档已经搬到Codelink_Legacy装饰图案。o, readCodelink()分配NA值点标记为“M”(MSR现货),“我”(不规则)和“C”(污染)。这可能会导致一些问题在大型数据集规范化。因为任何删除行包含NAs在正常化,当样本数量的增加删除rowa数量的增加,大幅减少的数量事实上的斑点/探测器中使用规范化。 Now, assigment of NA values is not performed anymore, the only exception being 'M' flagged spots, which have intensity values of -9999, and hence do not represent any measure of intensity. Many thanks to Emmanuelle Dantony for spotting this problem and subsequent feedback. o Background and normalization methods are applied calling the appropriate functions in the limma package. Support for type- and flag-based weights has been included, and weights are automatically created by readCodelinkSet(). Weights can be used to modulate the contribution of some probes to normalization and during linear modeling more efficiently. Examples on how to use these utilities are documented in the vignette Codelink_Introduction. o Added generic method normalize() for Codelink and CodelinkSet classes. Version 1.24.0 o Improvements on how codPlotScatter() manages labels. Renamed generic scatter plot function plotma() to plotxy(), which better reflects the current status. o Implemented missing function codPlotScatter() for CodelinkSet objects (accessible via codPlot(..., what = "scatter")). The implementation reuses the plotma() function used by codPlotMA(). By default the first array is plotted against the median. Thanks to William Michels for reporting this and testing the CodelinkSet framework. o Minor improvements to linear model section in CodelinkSet-vignette. Now the code is evaluated. Version 1.16.0 o Fixed check fail in windows machine by putting "multicore" in Enhancements, and checking if function "mclapply" is loaded. Addapted documentation to explain the new behavior. o Added missing file (averageProbes.Rd) to the svn. o Added CodelinkSetUnique class to store objects with unique probes. These objects use as featureNames the probe ID, and hence should be compatible with other packages that make use of featureNames() and the annotation packages. o Added function averageProbes() that computes the average of duplicated probes in the array. Currently is does the mean(). The standard deviation is computed too and stored in the slot "sd" (no accessor method at the moment). This computation requires time and therefore a call to mclapply() in multicore package is implemented through the optional argument 'parallel' (FALSE by default). Use of 'parallel = TRUE' is not recommended on GUI (like the Cocoa R.app) (see multicore package for issues with this). o Added '...' to readCodelinkSet() so that it pass additional arguments (e.g. 'flag') to readCodelink(). Thank you to Luca Beltrame for the suggestion and patch. o Now when readCodelinkSet() reads a list of files and the phenoData is not supplied it will create a default one, instead of failing. o Version number bumped for BioC devel branch. Version: 1.14.0 o Fixed bug in codCorrect() that would prevent the methods "half" and "subtract" for being available. Thanks to Fr?d?ric Boyer for reporting this. o Fixed warnings about missing (or suspect) links in documentation. Added tem- plate man page for CodelinkSet class. o Fixed warning on R CMD check about mismatch between objects and documentation.