paCalls(oligo)
paCalls()所属R语言包：oligo
Methods for P/A Calls
为P / A呼叫方法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Methods for Present/Absent Calls are meant to provide means of assessing whether or not each of the (PM) intensities are compatible with observations generated by background probes.
有/无检测的方法是为了提供评估是否（下午）强度与背景探针产生的意见兼容的手段。
用法----------Usage----------
paCalls(object, method, ..., verbose=TRUE)
## S4 method for signature 'ExonFeatureSet'
paCalls(object, method, verbose = TRUE)
## S4 method for signature 'GeneFeatureSet'
paCalls(object, method, verbose = TRUE)
## S4 method for signature 'ExpressionFeatureSet'
paCalls(object, method, ..., verbose = TRUE)
参数----------Arguments----------
参数：object
Exon/Gene/Expression-FeatureSet object.
外显子/基因/表达的FeatureSet对象。
参数：method
String defining what method to use. See 'Details'.
字符串定义使用什么方法。见“详细资料”。
参数：...
Additional arguments passed to MAS5. See 'Details'
额外的参数传递到MAS5。请参阅“详细资料”。
参数：verbose
Logical flag for verbosity.
冗长的逻辑标志。
Details
详情----------Details----------
For Whole Transcript arrays (Exon/Gene) the valid options for method are 'DABG' (p-values for each probe) and 'PSDABG' (p-values for each probeset). For Expression arrays, the only option currently available for method is 'MAS5'.
整个谈话阵列（外显子/基因）的有效选项methodDABG“（每个探针的p值）和”PSDABG（每个probeset的P-值）。表达阵列，method目前唯一的选择是MAS5“。
ABOUT MAS5 CALLS:
关于MAS5检测：
The additional arguments that can be passed to MAS5 are:
额外的参数，可以传递给MAS5是：
alpha1: a significance threshold in (0, alpha2);
alpha1：显着性阈值（0，alpha2）;
alpha2: a significance threshold in (alpha1, 0.5);
alpha2：显着性阈值（α1，0.5）;
tau: a small positive constant;
tau：一个小的正常数;
ignore.saturated: if TRUE, do the saturation correction described in the paper, with a saturation level of 46000;
ignore.saturated：如果为TRUE，在论文中描述的饱和度校正，做了46000的饱和程度;
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）。
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
值----------Value----------
A matrix (of dimension dim(PM) if method="DABG" or "MAS5"; of dimension length(unique(probeNames(object))) x ncol(object) if method="PSDABG") with p-values for P/A Calls.
（维暗淡（下午）如果method =“DABG”或“MAS5”维度的长度（独特（probeNames（对象）））x NCOL（对象），如果方法=“PSDABG”）与P-矩阵值的P / A呼叫。
作者（S）----------Author(s)----------
Benilton Carvalho
参考文献----------References----------
human exon microarrays. Genome Biol (2007) vol. 8 (4) pp. R64
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
举例----------Examples----------
## Not run: [＃无法运行：]
if (require(oligoData) & require(pd.huex.1.0.st.v2)){
data(affyExonFS)
## Get only 2 samples for example[＃获取只有2个样品例如]
dabgP = paCalls(affyExonFS[, 1:2])
dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG")
head(dabgP) ## for probe[＃探针]
head(dabgPS) ## for probeset[＃为probeset]
}
## End(Not run)[＃结束（不运行）]
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 2012-2-26 08:15:48
