filter.probes(Agi4x44PreProcess)
filter.probes()所属R语言包：Agi4x44PreProcess
Filtering out probes
过滤探测的
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Filter out probes according to their Quality Flag
筛选出探针根据其质量标志
用法----------Usage----------
filter.probes(ddNORM,control = NULL, wellaboveBG = NULL, isfound = NULL, wellaboveNEG = NULL, sat = NULL, PopnOL = NULL, NonUnifOL = NULL, nas = NULL, limWellAbove, limISF, limNEG, limSAT, limPopnOL, limNonUnifOL, limNAS, makePLOT, annotation.package, flag.counts = NULL, targets)
参数----------Arguments----------
参数：ddNORM
An RGList in log2 scale to be FILTERED out according to a Quality FLAG
根据质量标志被过滤掉以log2规模RGList
参数：control
LOGICAL: If True it removes controls
逻辑：如果为True删除控制
参数：wellaboveBG
LOGICAL: If True it filters by Well Above BG FLAG
逻辑：如果真远高于它的过滤器保函旗
参数：isfound
LOGICAL: If True it filters by Is Found FLAG
逻辑：如果为True，过滤被发现标志
参数：wellaboveNEG
LOGICAL: If True it filters by Well Above NEG CTRLS
逻辑：如果为True，过滤远高于南德CTRLS
参数：sat
LOGICAL: If True it filters by Is Saturated FLAG
逻辑：如果为True，过滤由饱和旗
参数：PopnOL
LOGICAL: If True it filters by Population Outlier FLAG
逻辑：如果人口离群标志真它的过滤器
参数：NonUnifOL
LOGICAL: If True it filters by Non Uniform Outlier FLAG
逻辑：如果真滤波器非均匀离群标志
参数：nas
LOGICAL: If True it removes NAs
逻辑：如果为True删除定居
参数：limWellAbove
for a given spot xi accros samples, is the minimum in a experimental condition with a wellaboveBG-FLAG = 1 (Is Well Above BG)
对于一个给定的专的第十一accros样本，是一个wellaboveBG旗在实验条件下的最低= 1（远高于BG是）
参数：limISF
for a given feature xi accros samples, is the minimum in a experimental condition with a isfound-FLAG = 1 (Is Found)
对于一个给定的功能第十一accros样品，在实验条件与isfound旗最低= 1（发现）
参数：limNEG
for a given feature xi accros samples, is the minimum in a experimental condition with a intensity > Limit established for negative controls (Mean + 1.5 x SD)
对于一个给定的功能第十一accros样本，是在实验条件下具有强度>限额为阴性对照组（平均+ 1.5×SD）设立最低
参数：limSAT
for a given feature xi accros samples, is the minimum in a experimental condition with a saturation-FLAG = 0 (Non Saturated)
对于一个给定的功能第十一accros样本，是在实验条件下的饱和标志最低= 0（非饱和）
参数：limPopnOL
for a given feature xi accros samples, is the minimum in a experimental condition with a saturation-FLAG = 1 (Is Pop OL)
对于一个给定的功能第十一accros样本，是在实验条件下的最低饱和标志= 1（这是流行的OL）
参数：limNonUnifOL
for a given feature xi accros samples, is the minimum in a experimental condition with a saturation-FLAG = 1 (Is Non Uni OL)
对于一个给定的功能第十一accros样本，是在实验条件下的最低饱和标志= 1（非统一的OL）
参数：limNAS
for a given feature xi accros samples, is the minimum in a experimental condition
对于一个给定的功能第十一accros样本，是在实验条件下的最低
参数：makePLOT
LOGICAL: If True it makes QC graphs filtering
逻辑：如果为True，它使过滤质量控制图
参数：annotation.package
a character specifying the AGI annotation package: 'hgug4112a.db','mgug4122a.db'
一个字符指定的AGI注解包：“hgug4112a.db，mgug4122a.db”
参数：flag.counts
LOGICAL: If True it runs the countFLAG function
逻辑：如果为True，它运行COUNTFLAG功能
参数：targets
data.frame with the target structure
数据框与目标结构
Details
详情----------Details----------
Agilent Feature Extraction software provides a flag for each spot that identifies different quantification errors of the signal. Quantification flags were used to filter out signals that did not reach a minimum established criterion of quality. Data were filtered at a probe level according to the following criteria. a- To keep features within the dynamic range of the scanner: For a spot = xi accross all the samples, we demand that at least p probes of the spot xi in at least one experimental condition had a quantification flag denoting that the signal is distinguishable from background. The same criterion is applied independently for the 'IsFound' flag and for signal saturation. b- To keep good quality features, we filtered out probes that had more than y in at least one experimental condition flagged as Outliers.
安捷伦特征提取软件提供了一个为每个点确定了不同的量化误差信号旗。量化标志被用来筛选出的信号，没有达到最低标准建立的质量。根据以下的标准数据进行过滤探针一级。一个扫描仪的动态范围内保持功能：对于现货=第十一accross所有的样品，我们要求，当场至少在一个实验条件第十一至少为p探针有一个量化的标志，表示该信号是有区别的从背景。同样的标准适用于独立“IsFound标志和信号饱和。 B-为了保持良好的质量特性，我们筛选出探针，在实验条件下至少有一个标记为离群小于y。
值----------Value----------
The function returns a RGList containing with the FILTERED data eliminated In order to allow the tracking of features that may have been filtered out from the original raw data, the following files are given:
该函数返回一个RGList为了消除可能已经从原始数据过滤功能允许跟踪筛选的数据含有下列文件：
RawDataNOCtrl.txt: contains all the features included in the array once the internal controls have been removed. Internal controls are removed prior to any preprocessing step.
RawDataNOCtrl.txt：包含一次的内部控制已被删除数组中的所有功能。内部控制被删除之前任何预处理步骤。
IsNOTWellAboveBG.txt: contains the features that have been filtered out because they are not distinguishable from the local background signal.
IsNOTWellAboveBG.txt：包含的功能已被过滤掉了，因为他们是从当地的背景信号区分。
We uses a Boolean flag indicating if a feature is WellAbove Background (Flag = 1) or not (Flag = 0). A feature reaches a Flag = 1 if IsPosAndSignif and additionally the gBGSubSignal is greater than 2.6*g(r)BG\_SD.
我们使用一个布尔标志，表示如果一个特点是WellAbove背景（旗= 1）或（标志= 0）。一种功能达到一个标志= 1，如果IsPosAndSignif和另外gBGSubSignal的是超过260克（R）BG \ _SD。
IsPosAndSignif uses a Boolean flag, established via a 2-sided t-test, indicates whether the mean signal of a feature is greater than the corresponding background. 1 indicates feature is positive and significant above background
IsPosAndSignif成立，通过双面t检验使用一个布尔标志，表示平均信号的功能是否是大于相应的背景。 1表示的特点是积极和显着的上述背景
IsNOTFound.txt: contains features that have been filtered out because were NOT FOUND. A feature is considered Found if two conditions are true: 1- the difference between the feature signal and the local background signal is more than 1.5 times the local background noise and 2- the spot diameter is at least 0.30 times the nominal spot diameter. A Boolean variable is used to flag found features. 1 = IsFound
IsNOTFound.txt：包含已被过滤掉，因为没有被发现的功能。被认为是一种功能，如果两个条件都为真：1 - 功能信号和本地背景信号之间的差异是1.5倍以上的本地背景噪声和2 - 光斑直径光斑直径至少0.30倍的名义。一个布尔变量用于标记的功能。 1 = IsFound
IsSaturated.txt: contains the features that are saturated. A feature is saturated IF 50 threshold. 1 = Saturated
IsSaturated.txt：含有饱和的特点。一个特点是饱和如果50的阈值。 1 =饱和
IsFeatNonUnifOL.txt: contains the features that are considered Non Uniformity Outlier. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a uniform feature. 1 indicates Feature is a non-uniformity outlier.
IsFeatNonUnifOL.txt：包含被视为非均匀性离群的功能。非均匀特征是像素噪音的功能，如果超过阈值建立了一个统一的功能。 1表示功能是一个非均匀离群。
IsFeatPopnOL.txt: contains the features that are considered Population Outlier. A feature is a population outlier if its signal intensity is lower than a lower threshold or exceeds an upper threshold determined using a multiplier (1.42) times the interquartile range of the population. 1 indicates Feature is a population outlier
IsFeatPopnOL.txt：包含被视为人口离群的功能。一个特点是人口离群值，如果它的信号强度低于阈值较低，或超过上限阈值确定使用乘数（1.42）倍人口的四分范围。 1表示的特点是人口离群
IsNOTWellAboveNEG.txt: Besides, for each feature we can demand a minimum signal value that have to be reached at least for a p in one of the experimental conditions. The minimum limit has been established as Mean Negative Controls + 1.5*(Std. dev.Negative Controls). Normally, after filtering by WellAboveBG and IsFound criteria, all probes are well above negative controls.
IsNOTWellAboveNEG.txt：此外，对于每一个功能，我们可以要求在实验条件之一鸭至少要达到最低信号值。平均阴性对照+ 1.5 *（标准dev.Negative控制）已建立最低限额。通常情况下，经过通过过滤WellAboveBG和IsFound标准，所有探针都远远高于阴性对照。
In addition to all files indicated above we have added ACCNUM, GENE SYMBOL, ENTREZID reference and gene DESCRIPTION corresponding to each manufacturer probe code in the corresponding annotation package.
此外所有的文件表明，上面我们已经加入ACCNUM基因符号ENTREZID的参考和基因描述对应到每个制造商在相应的注释包探针代码。
作者（S）----------Author(s)----------
Pedro Lopez-Romero
举例----------Examples----------
## Not run: [＃无法运行：]
data(dd)
data(targets)
library(hgug4112a.db)
ddNORM=BGandNorm(dd,BGmethod='half',NORMmethod='quantile',
foreground='MeanSignal',background='BGMedianSignal',
offset=50,makePLOTpre=FALSE,makePLOTpost=FALSE)
ddFILT=filter.probes(ddNORM,
control=TRUE,
wellaboveBG=TRUE,
isfound=TRUE,
wellaboveNEG=TRUE,
sat=TRUE,
PopnOL=TRUE,
NonUnifOL=TRUE,
nas=TRUE,
limWellAbove=75,
limISF=75,
limNEG=75,
limSAT=75,
limPopnOL=75,
limNonUnifOL=75,
limNAS=100,
makePLOT=TRUE,annotation.package="hgug4112a.db",flag.counts=TRUE,targets)
## 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。
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发表于 2012-2-25 11:34:16
