1.11.2版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - - - -阿BUG修复更新依赖引发事故。调查。Biomart似乎不再支持“hsapiens_gene_ensembl”(有时/错误)间歇性错误固定在后面Biomart版。o R 3.5.0支持GOCatEngine要求调整。R的变化版本1.7.1上- - - - - - - - - - - - - - - - - - - - - - - - - - - - BUG修复o sampleMeta可能负载因素,并使用字符串。以防止可能的sample-swapping,需要让所有输入作为字符串/ notfactors。我们可以内部力量。版本的变化就开始- - - - - - - - - - - - - - - - - - - - - - - - - - - - BUG修复o依赖GOSeq 1.23.2不再支持基因ID系统“refGene”,所以Entrez基因改变了IDs的名字“knownGene”。合并现在切断ENTREZ不是REFSEQ基因表。现在测试和基于R 3.3.0。 CHANGES IN VERSION 1.3.8 -------------------------- FEATURE o Adjusting the color thresholds for HMG diagram and Gamma scores to be properly scaled by dimensionality. Previous z-scoring method was occasionally making errors. Now a Gamma score of 1 indicates the distance between centroids, which would otherwise naturally scale by the square root of the geneset dimension. o Updated Vignette CHANGES IN VERSION 1.3.6 -------------------------- FEATURE o Simplified final output figure "HMG" and associated tables "HMG1" and "HMG2" calculate the distance to each centroid so the interpretation of results is simpler. Strong overlap to the HMA file. o Entries in the Vignette for this new 2 table output. CHANGES IN VERSION 1.3.4 -------------------------- BUG FIXES o Dependency GenomicRanges no longer exports "assay()" CHANGES IN VERSION 1.3.3 -------------------------- Rebuilt for R 3.2.2 BUG FIXES o Biomart.org went down for "ensembl" late 2015. now we ask "www.ensembl.org" directly for their mart. Resolves some warnings, and fixes ID collection. CHANGES IN VERSION 0.99.15 -------------------------- BUG FIXES o bugfix in gene ID systems passed to goseq. CHANGES IN VERSION 0.99.12 -------------------------- NEW FEATURES o expanding user manuals to clarify how figures and clustering is performed. CHANGES IN VERSION 0.99.11 --------------------------- BUG FIXES o bugfix in ProcessAll cardinality message. o Error catching around PCA. o Heatmap genelist now respects Annote_Filter file when LIMIT$HARD. o Cleaned up warnings when no rows for HMA. o Bugfix in PCA regarding non-negative definite covariance from princomp's eigen: replaced all instances with prcomp(). CHANGES IN VERSION 0.99.10 -------------------------- BUG FIXES o bugfix in G$LIMIT$baseMean and explanations of naming conventions in the vignette. CHANGES IN VERSION 0.99.4 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o replacing DESeq with DESeq2 Fall2014 CHANGES IN VERSION 0.0.0 ------------------------ NEW FEATURES o Release package. Fall 2014.