1.24版更改:BUG修复o删除了对r转换器的依赖。h 1.22版更改:用户可见的更改o改进了getProbeInfo()的结果;o fitPLM, coefs和残留物现在不存在。分别使用fitProbeLevelModel、coef和residuals。“coef”和“residuals”遵循R中其他地方使用的标准;修复了由oligoClasses有自己的annotation()方法导致的问题，当BiocGenerics添加了一个新的方法;修正了探测选择器，允许使用“目标”o PA Calls不知道目标;1.20版更改:USER VISIBLE Changes o新增getProbeInfo()函数，简化探针选择，无需使用SQL。o新增fitProbeLevelModel()函数。它允许探针级模型('plm'和'medianpolish')，可用于QC。 o fitPLM, coefs and resids are now Deprecated. Use fitProbeLevelModel, coef and residuals respectively. 'coef' and 'residuals' follow the standards used elsewhere in R. o Now using foreach for parallelization. BUG FIXES o Addressed issue in which probes without chr info would be removed from pmChr, leading to results whose dimensions did not match PM matrix (on TilingFeatureSet). Changes in version 1.18: USER VISIBLE CHANGES o pmStrand() now available for Affy-Tiling arrays (by Kristof De Beuf); BUG FIXES o Fixed message method when normalizing with large dataset support; Changes in version 1.16: USER VISIBLE CHANGES o Using NEWS.Rd; NEW FEATURES o New summarization methods are available: PLM, PLMr, PLMrr and PLMrc. These are implemented in the basicPLM function and also available through the summarize() interface (method=c('plm', 'plmr', 'plmrr', 'plmrc')); o fitPLM(), NUSE() and RLE() are now available; o Presence/Absence calls are available through paCalls(); o MAplot method with advanced options; BUG FIXES o 'pm<-', 'mm<-', 'bg<-' now work with ff_matrix replacements; o boxplot() now uses the correct (default) ylim if transfo != log2; o Fixed documentation for hist(), boxplot(), fitPLM(); o Fixed image for PLMset on NimbleGen arrays; Changes in version 1.14: USER VISIBLE CHANGES o Added support to read gzipped XYS files directly. o Added information for citation. o Added getNetAffx method to retrieve NetAffx annotation for Exon ST and Gene ST arrays. o Reading in uncompressed XYS files is much faster than in 1.12.2. o Added vignette for Exon/Gene ST arrays (rma and NetAffx annot) BUG FIXES o Fixed bug in boxplot / hist / MAplot o Fixed issue that would appear with GeneFeatureSet objects, in which it selections like obj[c(2, 2, 1),] would generate invalid GeneFeatureSet objects o Fixed bugs in image / bg / bgindex / bgSequence for Exon and Gene arrays (due to changes in annotation) o Added date/time of scan (for XYS/CEL files) to the protocolData slot. For 1 channel applications, the field is called 'dates'; for 2 channel apps, there are 2 fields: 'dates1' and 'dates2' NEW FEATURES o New method, runDate(), to extract scan dates from FeatureSet objects Changes in version 1.11: USER VISIBLE CHANGES o New vignette structure: Vignette 1: Overview (with multiple examples) Vignette 2: Expression (NimbleGen data) Vignette 3: SNP Genotyping (Affymetrix) o Uses Imports rather than Depends. Users must explicitly load Biobase, affyio, preprocessCore if they need functions from these packages. o Revised man page for rma. NEW FEATURES o Support to large datasets via ff package. The user should load the ff package in order to use this feature. Files used by ff are saved to getwd(), unless the user changes the standard path. o Support to parallel computing via snow package. The user should load *both* ff and snow in order to use the parallel features implemented in the package (backgroundCorrect, normalize, summarize, rma, normalizeToTarget). Cluster variable should be set as options(cluster=makeCluster(...)). o seqColors and darkColors, respectively, generate a vector of sequential colors (in blue) and (qualitative) dark colors (based onn Dark2 from RColorBrewer). o plotM method for SnpSuperSet (plot genotype clusters). o getAffinitySplineCoefficients estimates the affinity spline coefficients. o getBaseProfile estimates and optionally plots sequence effect like gcrma. BUG FIXES o Fixed definition for probeNames() for Exon/Gene arrays. (Mikhail Pachkov)