ilm(affyILM)
ilm()所属R语言包：affyILM
affyILM
affyILM
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function is the working horse of the package and is used as an overall function to calculate the background intensities as well as the concentrations.
此功能是包马工作，并作为一个整体功能是用来计算背景强度以及浓度。
用法----------Usage----------
ilm(celfiles,satLim=10000,scale.method="linear",scale.target="concs",cdf.name=NULL,probe.table=NULL,probe.name=NULL,na.replace=NULL,bgcorrect=F,summarize.level="none",summary.method="none",summary.na.rm=TRUE,dgDRpairs=NULL,dgRRpairs=NULL,beta=NULL)
参数----------Arguments----------
参数：celfiles
filenames of CEL-files
为CEL文件的文件名
参数：satLim
Saturation Limit of the Langmuir isotherm (determined by scanner). Default value 10000.
Langmuir等温的饱和极限（扫描仪确定）。默认值为10000。
参数：scale.method
Method used to scale the values between arrays. "linear" (default) uses a coefficient to adjust slopes of all pairwise comparisons to unity, and "linear.stat" makes use of both median and median absolute deviation to scale the values.
方法用于扩展阵列之间的值。 “线性”（默认）使用系数调整所有成对比较统一的斜坡，和“linear.stat”的使用缩放值中位数和中位数绝对偏差。
参数：scale.target
Specify on which value the scaling step has to be performed. Authorized values are "intens" and "concs", respectively refering to probe intensities and probe concentrations.
指定价值缩放步骤进行。授权值“intens”和“concs”，分别参考探测强度和探针浓度。
参数：cdf.name
Name of a package providing the chip definition file. By default, this information is extracted from the chip-model provided by the CEL files. This parameter can be used to specify alternative definition files.
提供芯片定义文件包的名称。默认情况下，此信息提取从CEL文件所提供的芯片模型。此参数可用于指定替代的定义文件。
参数：probe.table
A matrix providing probe annotation table, with the same structure than the probe package provided on Bioconductor. Manual creation of probe tables, or subsets, can be used in place of alternative definition files and probe packages. An additional column, named "Cluster.Set.Name", can be added for new whole-gene arrays.
矩阵提供探针注释表，与比上Bioconductor提供的探测包的结构相同。手动创建探针表，或子集，可以用来替代定义文件和探针包的地方。一个额外的列，名为“Cluster.Set.Name”，可以添加新的全基因阵列。
参数：probe.name
Name of a package providing the probe annotation table. By default, this information is extracted from the chip-model provided by the CEL files. This parameter can be used to specify alternative probe table packages.
一个提供探针注释表的包的名称。默认情况下，此信息提取从CEL文件所提供的芯片模型。此参数可用于指定替代探针表包。
参数：na.replace
Experimental. The methods that can be used to replace missing values, for each probe set. na.replace should be a list with 2 slots, each containing a function. The first slot should contain the function used to missing probe concentrations due to missing probe intensities (i.e. median), and the second slot should contain the function used to compute probe concentrations when the missing value is due to intensity values that are higher than the saturation limit defined by satLim (i.e. max). Those function are then used to compute replacement values based on concentration values of the same probe set.
实验。可以用来取代遗漏值的方法，为每个探针设置。 na.replace应该是2个插槽，每个包含一个函数列表。第一槽应包含用来失踪由于缺少探针强度（即中位数）的探针浓度的功能，第二个插槽应该包含用于计算探针浓度的功能，缺少的值时，是由于强度值高于饱和限制定义由satLim（即最大值）。然后，这些功能是用来计算上相同的探针集的浓度值的替换值。
参数：bgcorrect
Not used in the current release. Default value is FALSE. This parameter will be use in the next releases to compute the background correction.
在当前版本中不使用。默认值为FALSE。此参数将在未来版本中使用的背景校正计算。
参数：summarize.level
Parameter for summarization (character). Default value is "none", to avoid this step. Other accepted values are "probeset" for traditionale definition of probe sets, "cluster" if a Cluster.Set.Name column has been manually added to the probe table and provided with parameter probe.table, or "both" to run summarization using both definitions.
综述参数（字符）。默认值是“无”，以避免这一步。其他接受值都是“probeset”探针定义traditionale的设置，“聚类”已如果Cluster.Set.Name列手动添加探针表，并提供参数probe.table“或”both“使用两种定义运行总结。
参数：summary.method
Parameter for summarization (character). Default value is "none", to avoid this step. Other accepted values are "median" to use the median of probe concentrations, "medpolish" to use the medianpolish on the log2 of concentrations, and "tmedpolish" for the transposed medianpolish procedure.
综述参数（字符）。默认值是“无”，以避免这一步。其他公认的价值观是“中位数”使用探针浓度的中位数，的“medpolish”上使用浓度的log2 medianpolish，和“tmedpolish的”换位medianpolish过程的。
参数：summary.na.rm
Parameter for summarization (logical). Default value is TRUE, sothat to be able to compute summarized values when data contains missing values.
综述参数（逻辑）。默认值是TRUE时，充分使用，以便能够计算汇总值数据时，包含遗漏值。
参数：dgDRpairs
Experts only. Allow to tune the computation of DNA/RNA hybridization free energies. dgDRpairs is used to provide list of deltaG values for di-nucleotides.
专家只。允许调整的DNA / RNA杂交自由能计算。用于dgDRpairs的列表，deltaG DI-核苷酸值提供。
参数：dgRRpairs
Experts only. Allow to tune the computation of RNA/RNA hybridization free energies. dgRRpairs is used to provide list of deltaG values for di-nucleotides.
专家只。允许调整RNA / RNA杂交自由能计算。用于dgRRpairs的列表，deltaG DI-核苷酸值提供。
参数：beta
Experts only. Allow to tune the computation of concentrations using the Langmuir Isotherm. beta = 1/RT allow to change the effective hybridization temperature.
专家只。允许调整使用Langmuir等温浓度的计算。 β= 1/RT允许的改变有效的杂交温度。
Details
详情----------Details----------
The Langmuir Isotherm is used as a model to estimate probe concentrations from measured PM intensities, thanks to the computation of sequence-specific DNA/RNA hybridization free energies.
Langmuir等温被用来作为模型估计探针浓度测量时的强度，由于特定序列的DNA / RNA杂交自由能计算。
值----------Value----------
An object of class ILM
一个对象的类ILM
注意----------Note----------
The AffymetrixDataTestFiles-package must be installed to run examples.
必须安装的AffymetrixDataTestFiles包运行的例子。
作者（S）----------Author(s)----------
Myriam Kroll, Fabrice Berger, Gerard Barkema and Enrico Carlon
参考文献----------References----------
G Mulders, GT Barkema and E Carlon, Inverse Langmuir method for oligonucleotide microarray analysis, BMC Bioinformatics (2009) 10, 64
参见----------See Also----------
getIntens, getProbeConcs, getExprSummary, getSDSummary
getIntens，getProbeConcs，getExprSummary，getSDSummary
举例----------Examples----------
## Locate and read in CEL-file[＃找到并读取CEL - 文件]
path <- system.file("rawData", "FusionSDK_HG-Focus", "HG-Focus", "2.Calvin",
package="AffymetrixDataTestFiles")
file1 <- file.path(path,"HG-Focus-1-121502.CEL")
## Calculation of background estimates and expression values (concentrations)[＃背景估计和表达值（浓度计算）]
result <- ilm(file1)
## show all[＃显示所有]
show(result)
## per probeset (example probeset randomly chosen)[＃每probeset（例如probeset随机选择）]
result["AFFX-r2-P1-cre-5_at"]
## Analysis of two files[＃两个文件的分析]
file2 <- file.path(path,"HG-Focus-2-121502.CEL")
result2 <- ilm(c(file1,file2))
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 11:16:32
