芯片探针ID注释平台R包的对应关系

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芯片探针ID注释平台R包的对应关系,第1张

GPL201hgfocus [HG-Focus] Affymetrix Human HG-Focus Target Array

GPL96hgu133a [HG-U133A] Affymetrix Human Genome U133A Array

GPL571hgu133a2[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array

GPL97hgu133b [HG-U133B] Affymetrix Human Genome U133B Array

GPL570hgu133plus2 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

GPL13667hgu219 [HG-U219] Affymetrix Human Genome U219 Array

GPL8300hgu95av2[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array

GPL91hgu95av2[HG_U95A] Affymetrix Human Genome U95A Array

GPL92hgu95b [HG_U95B] Affymetrix Human Genome U95B Array

GPL93hgu95c [HG_U95C] Affymetrix Human Genome U95C Array

GPL94hgu95d [HG_U95D] Affymetrix Human Genome U95D Array

GPL95hgu95e [HG_U95E] Affymetrix Human Genome U95E Array

GPL887hgug4110b Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)

GPL886hgug4111a Agilent-011871 Human 1B Microarray G4111A (Feature Number version)

GPL1708hgug4112a Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)

GPL13497HsAgilentDesign026652 Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)

GPL6244hugene10sttranscriptcluster [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]

GPL11532hugene11sttranscriptcluster [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]

GPL6097illuminaHumanv1 Illumina human-6 v1.0 expression beadchip

GPL6102illuminaHumanv2 Illumina human-6 v2.0 expression beadchip

GPL6947illuminaHumanv3 Illumina HumanHT-12 V3.0 expression beadchip

GPL10558illuminaHumanv4 Illumina HumanHT-12 V4.0 expression beadchip

GPL6885illuminaMousev2 Illumina MouseRef-8 v2.0 expression beadchip

GPL81mgu74av2[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array

GPL82mgu74bv2[MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array

GPL83mgu74cv2[MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array

GPL339moe430a [MOE430A] Affymetrix Mouse Expression 430A Array

GPL6246mogene10sttranscriptcluster [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]

GPL340mouse4302 [MOE430B] Affymetrix Mouse Expression 430B Array

GPL1261mouse430a2 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array

GPL8321mouse430a2 [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array

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看注释前的字母。

R语言初学指南可在脚本中加入注释。在脚本中,任何以“#”(sharp/numbersymbol)开头的命令行都会被R忽略。

同样,若“#”出现在某行的中间,则该行中“#”后面的语句都会被忽略。可利用这一特性对脚本添加注释,以便用户或他人日后查阅。

例如,作者每次查看前一天编写的脚本时,都要重新梳理并回忆每条脚本语句的作用。

在基因芯片数据或其他类型数据中,采用计算所有样本的平均值从而进行填充,如果需要用中位数或其他统计量填充时只需修改相应的方法即可

#1. 检查是否有缺失值

which(is.na(mRNA),arr.ind = T)

#2. 计算行均值并填充

#该数据中探针(基因)为行(名),样本为列(名),(数据框内容为表达量数据值型数据数据)格式可见文章最后

row_mean <- apply(mRNA,1,mean,na.rm =T) #1是行,2是列,若用其他方法修改mean即可

mRNA$MEAN <- row_mean

ncol = 样本数

for (i in 1:nrow(mRNA)) {

  mRNA[i,is.na(mRNA[i,])] <- mRNA[i,ncol]

}