mas5calls(affy)
mas5calls()所属R语言包：affy
MAS 5.0 Absolute Detection
MAS 5.0绝对检测
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs the Wilcoxon signed rank-based gene expression presence/absence detection algorithm first implemented in the Affymetrix Microarray Suite version 5.
执行Wilcoxon符号秩的基因表达存在/不存在的检测算法，首先在实施的Affymetrix芯片套件版本5。
用法----------Usage----------
mas5calls(object,...)
mas5calls.AffyBatch(object, ids = NULL, verbose = TRUE, tau = 0.015,
alpha1 = 0.04, alpha2 = 0.06,
ignore.saturated=TRUE)
mas5calls.ProbeSet(object, tau = 0.015, alpha1 = 0.04, alpha2 = 0.06,
ignore.saturated=TRUE)
mas5.detection(mat, tau = 0.015, alpha1 = 0.04, alpha2 = 0.06,
exact.pvals = FALSE, cont.correct = FALSE)
参数----------Arguments----------
参数：object
an object of class AffyBatch or ProbeSet.
类AffyBatch或ProbeSet的对象。
参数：ids
probeset IDs for which you want to compute calls.
为您要计算呼叫probeset标识。
参数：mat
an n-by-2 matrix of paired values (pairs in rows), PMs first col.
一个n-2配对值矩阵（双行中），PMS第一山坳。
参数：verbose
logical. It TRUE, status of processing is reported.
逻辑。 TRUE，处理状态报告。
参数：tau
a small positive constant.
一个小的正数。
参数：alpha1
a significance threshold in (0, alpha2).
显着性阈值（0，alpha2）。
参数：alpha2
a significance threshold in (alpha1, 0.5).
显着性阈值（α1，0.5）。
参数：exact.pvals
logical controlling whether exact p-values are computed (irrelevant if n<50 and there are no ties). Otherwise the normal approximation is used.
逻辑控制是否精确p值计算（无关当n <50，有没有关系）。否则，正常使用近似。
参数：ignore.saturated
if TRUE, do the saturation correction described in the paper, with a saturation level of 46000.
如果为true，在论文中描述的饱和度校正，与46000饱和水平。
参数：cont.correct
logical controlling whether continuity correction is used in the p-value normal approximation.
逻辑控制是否连续性校正p值正常逼近。
参数：...
any of the above arguments that applies.
任何适用于上述论点。
Details
详情----------Details----------
This function performs the hypothesis test:
执行此功能的假设检验：
H0: median(Ri) = tau, corresponding to absence of transcript H1: median(Ri) > tau, corresponding to presence of transcript
H 0：中位数（RI）=头，相应转录H1的情况下：中位数（RI）>头，相应成绩单的存在
where Ri = (PMi - MMi) / (PMi + MMi) for each i a probe-pair in the probe-set represented by data.
RI =（PMI - MMI）为探针对每个数据代表的探针集的IA /（PMI + MMI）。
Currently exact.pvals=TRUE is not supported, and cont.correct=TRUE works but does not give great results (so both should be left as FALSE). The defaults for tau, alpha1 and alpha2 correspond to those in MAS5.0.
目前exact.pvals = TRUE不支持，cont.correct = TRUE，作品，但不给伟大的结果（这样既应留为FALSE）。头，alpha1和alpha2默认对应那些MAS5.0。
The p-value that is returned estimates the usual quantity:
返回的p值估计通常的数量：
Pr(observing a more "present looking" probe-set than data | data is absent)
镨（观察寻找更多的“礼物”探针比数据数据是缺席）
So that small p-values imply presence while large ones imply absence of transcript. The detection call is computed by thresholding the p-value as in:
让小p值意味着存在，而路数意味着没有成绩单。检测检测阈值的P-值，如计算：
call "P" if p-value < alpha1 call "M" if alpha1 <= p-value < alpha2 call "A" if alpha2 <= p-value
所谓的“P”字如果p值<甲一呼吁的“M”如果甲一<= p值<alpha2呼叫“，”如果alpha2 <= P-值
This implementation has been validated against the original MAS5.0 implementation with the following results (for exact.pvals and cont.correct set to F):
本实施已对原MAS5.0实施验证，结果如下（为exact.pvals和cont.correct设置到F）：
Average Relative Change from MAS5.0 p-values:38% Proportion of calls different to MAS5.0 calls:1.0%
从MAS5.0 p值的平均相对变化：38％的比例要求不同MAS5.0检测：1.0％
where "average/proportion" means over all probe-sets and arrays, where the data came from 11 bacterial control probe-sets spiked-in over a range of concentrations (from 0 to 150 pico-mols) over 26 arrays. These are the spike-in data from the GeneLogic Concentration Series Spikein Dataset.
“平均/比例”意味着所有探针和阵列，其中的数据来自11个细菌控制探针设置钉在很大的浓度范围超过26阵列（从0到150微微莫尔斯）。这些都是秒杀的GeneLogic浓度的系列Spikein数据集从数据。
Clearly the p-values computed here differ from those computed by MAS5.0 – this will be improved in subsequent releases of the affy package. However the p-value discrepancies are small enough to result in the call being very closely aligned with those of MAS5.0 (99 percent were identical on the validation set) – so this implementation will still be of use.
显然，这里计算的P-值不同于那些计算机MAS5.0 - 这将在后续版本的affy包改善。然而，P-值不符，小到足以导致非常密切对齐（99％是相同的验证集）的MAS5.0通话 - 所以这个实现仍然是使用。
The function mas5.detect is no longer the engine function for the others. C code is no available that computes the Wilcox test faster. The function is kept so that people can look at the R code (instead of C).
功能mas5.detect已不再是别人的引擎功能。 C代码是没有可用的计算威尔科克斯测试速度更快。保持该功能，使人们可以期待在R代码（而不是C）。
值----------Value----------
mas5.detect returns a list containing the following components:
mas5.detect返回一个列表，其中包含以下组件：
参数：pval
a real p-value in [0,1] equal to the probability of observing probe-level intensities that are more present looking than data assuming the data represents an absent transcript; that is a transcript is more likely to be present for p-values closer 0.
在[0,1]真正的p值等于观察更比数据假设数据代表缺席的成绩单的探针级强度的概率;谈话是p值更可能是目前接近0。
参数：call
either "P", "M" or "A" representing a call of present, marginal or absent; computed by simply thresholding pval using alpha1 and alpha2.
无论是“P”字，“M”或“一”代表的呼叫目前，边际或缺席，由简单的阈值pval的使用alpha1和alpha2计算。
The mas5calls method for AffyBatch returns an ExpressionSet with calls accessible with exprs(obj) and p-values available with assayData(obj)[["se.exprs"]]. The code mas5calls for ProbeSet returns a list with vectors of calls and p-values.
的mas5calls AffyBatch方法返回一个呼叫与ExpressionSet访问和P-值与exprs(obj)的assayData(obj)[["se.exprs"]]。代码mas5callsProbeSet检测和p值的向量返回列表。
作者（S）----------Author(s)----------
Crispin Miller, Benjamin I. P. Rubinstein, Rafael A. Irizarry
参考文献----------References----------
S. and Webster, T. A. and Harrington, C. A. and Ho, M. H. and Baid, J. and Smeekens, S. P. (2002) Analysis of high density expression microarrays with signed-rank call algorithms, Bioinformatics, 18(12), pp. 1593–1599.
Ryder, T. (2001) Rank-based algorithms for analysis of microarrays, Proceedings of SPIE, Microarrays: Optical Technologies and Informatics, 4266.
Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf, http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf
举例----------Examples----------
if (require(affydata)) {
data(Dilution)
PACalls <- mas5calls(Dilution)
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 11:27:38
