包:codelink ====================版本1.38.0 o修正错误读取选项类型=“原始”或类型=“规范”的codelink文件。o现在readCodelinkSet()接受"path="作为参数来允许从目标目录读取文件。版本1.32.0 o对文档的小修正。o从DESCRIPTION文件中删除了旧的术语“Bioarray”(最初用于第一个Codelink平台)。版本1.30.0 o CodelinkSet类已被采用为官方支持的类，用于存储Codelink数据。关于这个主题的文档已经改进，并且有一个新的描述CodelinkSet接口的小插图可用(Codelink_Introduction)。旧Codelink类的文档已经移到Codelink_Legacy小插图中。o在此之前，readCodelink()将NA值分配给标记为“M”(MSR点)，“I”(不规则)和“C”(污染)的点。在标准化过程中，这可能会导致大型数据集出现一些问题。因为在归一化过程中，任何包含NAs的行都会被移除，当样本数量增加时，被移除的rowa数量也会增加，从而大大减少归一化过程中使用的事实上的点/探针的数量。 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.