Agreement of differential expression analysis
协议的差异表达分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The objective of AGDEX is to evaluate whether the results of a pair of two-group differential expression analysis comparisons show a level of agreement that is greater than expected if the group labels for each two-group comparison are randomly assigned. The agreement is evaluated for the entire transcriptome and (optionally) for a collection of pre-defined gene-sets. Additionally, the procedure performs permutation-based differential expression and meta analysis at both gene and gene-set levels of the data from each experiment.
的AGDEX的目标是，以评估是否对两个组的差异表达分析比较，结果表明协议是大于预期，如果每两个组比较组标签被随机分配水平。该协议被评为整个转录组和预先定义的基因组的集合（可选）。此外，程序进行置换的差异表达基因和基因组水平从每个实验数据和meta分析。
list of main functions:
主要功能列表：
make.dex.set.object: a function to generate a list object for agdex() function
make.dex.set.object：一个函数来生成一个列表对象agdex（）函数
agdex: a function to perform AGDEX analysis
agdex：一个函数执行AGDEX分析
agdex.scatterplot: a function to plot the results of AGDEX analysis for visualization
agdex.scatterplot：绘制AGDEX分析结果的可视化功能
get.gset.result.details: a function to obtain gene level detaills for specified one gene-set or multiple gene-sets
get.gset.result.details：获得指定的一个基因组或多个基因组基因水平detaills的功能
write.agdex.result: a function to write the AGDEX result to a tab-delimited text file
write.agdex.result：到写的AGDEX的结果以制表符分隔的文本文件的功能
read.agdex.result: a function to read the AGDEX result from an output file written by write.agdex.result
read.agdex.result：读从由write.agdex.result写了一个输出文件AGDEX结果功能
write.agdex.gset.details: a function to write a tab-delimited text file with the gene-level details for the results of a gene-set analysis
write.agdex.gset.details：功能与基因组分析的结果，基因层次的细节写一个制表符分隔的文本文件
read.agdex.gset.details: a function to read the output file generated by write.agdex.gset.details
read.agdex.gset.details：一个函数来读取输出文件write.agdex.gset.details产生
Details
详情----------Details----------
AGDEX combines the differential expression analysis results from a pair of two-group comparisons. The two comparisons may utilize different species or platforms. AGDEX has been used to confirm that new mouse models accurately represent the transcriptomes of the pediatric brain tumors ependymoma (Johnson et al. 2010) and medulloblastoma (Gibson et al. 2010). Pounds et al. (2011) provide a detailed description of the AGDEX procedure. In summary, AGDEX analysis can perform the following analysis:
AGDEX结合从一两个组比较差异表达分析结果。两个比较可能利用不同的物种或平台。已被用于AGDEX，以确认新的小鼠模型准确地反映小儿脑肿瘤室管膜瘤（Johnson等，2010）和髓母单元瘤（Gibson等，2010）的转录。英镑等。 （2011）提供了一个的AGDEX过程的详细描述。总之，AGDEX分析可以执行以下分析：
1. identify individual genes that are differentially expressed for each two-group comparison;
1。确定个人每两个组比较，差异表达的基因;
2. identify gene-sets that are differentially expressed for each two-group comparison;
2。确定每两个组比较，差异表达的基因组;
3. integrate results across the pair of two-group comparisons to identify differentially expressed genes;
3。整个对两个组进行比较，找出差异表达基因整合的结果;
4. integrate results across the pair of two-group comparisons to identify differentially expressed gene-sets;
4。整个对两个组进行比较，找出差异表达的基因组整合的结果;
5. characterize and determine the statistical significance of similarities of differential expression profiles across the pair of two-group comparisons for the entire transcriptome and for specific gene-sets.
5。表征和确定整个对整个特定的基因组的转录和两个组比较差异表达谱的相似的统计意义。
作者（S）----------Author(s)----------
Stan Pounds <<a href="mailto:stanley.pounds@stjude.org">stanley.pounds@stjude.org</a>>; Cuilan Lani Gao <<a href="mailto:cuilan.gao@stjude.org">cuilan.gao@stjude.org</a>>
参考文献----------References----------
A procedure to statistically evaluate agreement of differential expression for cross-species genomics. Bioinformatics doi: 10.1093/bioinformatics/btr362 (2011).
发表于 2012-2-25 11:31:12
