有一篇文章“Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data”，提到了“Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses 40 may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions”，意思是说原始的Affymetrix探针组定义是不准确、过时的，要重定义探针组（Custom CDF）。

重定义的格式包括：

名称

含义

ENTREZG

REFSEQ

ENSG

ENSE

ENST

VEGAG

VEGAE

VEGAT

TAIRG

TAIRT

UG

MIRBASEF

MIRBASEG

物种包括：

名称

含义

简写

Anopheles gambiae

冈比亚疟蚊

Ag

Arabidopsis thaliana

拟南芥

At

Bos taurus

牛

Bt

Caenorhabditis elegans

秀丽隐杆线虫

Ce

Canis familiaris

犬类

Cf

Danio rerio

鲐鱼类

Dr

Drosophila melanogaster

黑腹果蝇

Dm

Gallus gallus

原鸡

Gg

Homo sapiens

人类

Hs

Macaca mulatta

猕猴

MAmu

Mus musculus

小家鼠

Mm

Oryza sativa

稻

Os

Rattus norvegicus

鼠类

Rn

Saccharomyces cerevisiae

酿酒酵母

Sc

Schizosaccharomyces pombe

粟酒裂殖酵母

Sp

Sus scrofa

野猪

Ss

在“02、CDF文件”中提到过，每种型号的芯片都有着对应CDF包，那么重定义后CDF的名称命名如下（加号代表连接，不要写进去）：

原CDF包名+物种简写小写+格式名小写

如HG-U133_Plus_2阵列原本对应hgu133plus2包，如果选择了Homo sapiens（人类物种），ENSG格式，那么就对应hgu133plus2hsensgcdf包了。

获取hgu133plus2的探针组名称，可以：

library(affy)     ## 导入affy包

cdfname <- "hgu133plus2"

cdfname <-"hgu133plus2hsensgcdf"

how = getOption("BioC")$affy$probesloc

verbose = FALSE

badOut <- list()

for (i in :length(how))

{

    cur <- how[[i]]

        envir <- switch(cur$what,

        environment = cdfFromEnvironment(cdfname, cur$where, verbose),

        libPath = cdfFromLibPath(cdfname, cur$where, verbose = verbose),

        bioC = cdfFromBioC(cdfname, cur$where, verbose))

}

genenames <- ls(envir)        ## 探针组名称

> length(genenames)        ## 探针组个数

[]

> genenames[:]        ## 输出前100个探针组名称

  [] "1007_s_at"    "1053_at"      "117_at"       "121_at"

  [] "1255_g_at"    "1294_at"      "1316_at"      "1320_at"

  [] "1405_i_at"    "1431_at"      "1438_at"      "1487_at"

 [] "1494_f_at"    "1552256_a_at" "1552257_a_at" "1552258_at"

 [] "1552261_at"   "1552263_at"   "1552264_a_at" "1552266_at"

 [] "1552269_at"   "1552271_at"   "1552272_a_at" "1552274_at"

 [] "1552275_s_at" "1552276_a_at" "1552277_a_at" "1552278_a_at"

 [] "1552279_a_at" "1552280_at"   "1552281_at"   "1552283_s_at"

 [] "1552286_at"   "1552287_s_at" "1552288_at"   "1552289_a_at"

 [] "1552291_at"   "1552293_at"   "1552295_a_at" "1552296_at"

 [] "1552299_at"   "1552301_a_at" "1552302_at"   "1552303_a_at"

 [] "1552304_at"   "1552306_at"   "1552307_a_at" "1552309_a_at"

 [] "1552310_at"   "1552311_a_at" "1552312_a_at" "1552314_a_at"

 [] "1552315_at"   "1552316_a_at" "1552318_at"   "1552319_a_at"

 [] "1552320_a_at" "1552321_a_at" "1552322_at"   "1552323_s_at"

 [] "1552325_at"   "1552326_a_at" "1552327_at"   "1552329_at"

 [] "1552330_at"   "1552332_at"   "1552334_at"   "1552335_at"

 [] "1552337_s_at" "1552338_at"   "1552340_at"   "1552343_s_at"

 [] "1552344_s_at" "1552347_at"   "1552348_at"   "1552349_a_at"

 [] "1552354_at"   "1552355_s_at" "1552359_at"   "1552360_a_at"

 [] "1552362_a_at" "1552364_s_at" "1552365_at"   "1552367_a_at"

 [] "1552368_at"   "1552370_at"   "1552372_at"   "1552373_s_at"

 [] "1552375_at"   "1552377_s_at" "1552378_s_at" "1552379_at"

 [] "1552381_at"   "1552383_at"   "1552384_a_at" "1552386_at"

 [] "1552388_at"   "1552389_at"   "1552390_a_at" "1552391_at"

获取hgu133aplus2_Hs_ENSG的探针组名称，把上面的cdfname换成"hgu133plus2hsensgcdf"即可，最后得到以下结果：

> length(genenames)    ## 重定义后的探针组数目

[]

> genenames[:]        ## 重定义后的探针组名称的前100个

  [] "AFFX-BioB-3_at"              "AFFX-BioB-5_at"

  [] "AFFX-BioB-M_at"              "AFFX-BioC-3_at"

  [] "AFFX-BioC-5_at"              "AFFX-BioDn-3_at"

  [] "AFFX-BioDn-5_at"             "AFFX-CreX-3_at"

  [] "AFFX-CreX-5_at"              "AFFX-DapX-3_at"

 [] "AFFX-DapX-5_at"              "AFFX-DapX-M_at"

 [] "AFFX-HSAC07/X00351_3_at"     "AFFX-HSAC07/X00351_5_at"

 [] "AFFX-HSAC07/X00351_M_at"     "AFFX-hum_alu_at"

 [] "AFFX-HUMGAPDH/M33197_3_at"   "AFFX-HUMGAPDH/M33197_5_at"

 [] "AFFX-HUMGAPDH/M33197_M_at"   "AFFX-HUMISGF3A/M97935_3_at"

 [] "AFFX-HUMISGF3A/M97935_5_at"  "AFFX-HUMISGF3A/M97935_MA_at"

 [] "AFFX-HUMISGF3A/M97935_MB_at" "AFFX-HUMRGE/M10098_3_at"

 [] "AFFX-HUMRGE/M10098_5_at"     "AFFX-HUMRGE/M10098_M_at"

 [] "AFFX-LysX-3_at"              "AFFX-LysX-5_at"

 [] "AFFX-LysX-M_at"              "AFFX-M27830_3_at"

 [] "AFFX-M27830_5_at"            "AFFX-M27830_M_at"

 [] "AFFX-PheX-3_at"              "AFFX-PheX-5_at"

 [] "AFFX-PheX-M_at"              "AFFX-r2-Bs-dap-3_at"

 [] "AFFX-r2-Bs-dap-5_at"         "AFFX-r2-Bs-dap-M_at"

 [] "AFFX-r2-Bs-lys-3_at"         "AFFX-r2-Bs-lys-5_at"

 [] "AFFX-r2-Bs-lys-M_at"         "AFFX-r2-Bs-phe-3_at"

 [] "AFFX-r2-Bs-phe-5_at"         "AFFX-r2-Bs-phe-M_at"

 [] "AFFX-r2-Bs-thr-3_s_at"       "AFFX-r2-Bs-thr-5_s_at"

 [] "AFFX-r2-Bs-thr-M_s_at"       "AFFX-r2-Ec-bioB-3_at"

 [] "AFFX-r2-Ec-bioB-5_at"        "AFFX-r2-Ec-bioB-M_at"

 [] "AFFX-r2-Ec-bioC-3_at"        "AFFX-r2-Ec-bioC-5_at"

 [] "AFFX-r2-Ec-bioD-3_at"        "AFFX-r2-Ec-bioD-5_at"

 [] "AFFX-r2-P1-cre-3_at"         "AFFX-r2-P1-cre-5_at"

 [] "AFFX-ThrX-3_at"              "AFFX-ThrX-5_at"

 [] "AFFX-ThrX-M_at"              "AFFX-TrpnX-3_at"

 [] "AFFX-TrpnX-5_at"             "AFFX-TrpnX-M_at"

 [] "ENSG00000000003_at"          "ENSG00000000005_at"

 [] "ENSG00000000419_at"          "ENSG00000000457_at"

 [] "ENSG00000000460_at"          "ENSG00000000938_at"

 [] "ENSG00000000971_at"          "ENSG00000001036_at"

 [] "ENSG00000001084_at"          "ENSG00000001167_at"

 [] "ENSG00000001460_at"          "ENSG00000001461_at"

 [] "ENSG00000001497_at"          "ENSG00000001561_at"

 [] "ENSG00000001617_at"          "ENSG00000001626_at"

 [] "ENSG00000001629_at"          "ENSG00000001631_at"

 [] "ENSG00000002016_at"          "ENSG00000002079_at"

 [] "ENSG00000002330_at"          "ENSG00000002549_at"

 [] "ENSG00000002586_at"          "ENSG00000002587_at"

 [] "ENSG00000002726_at"          "ENSG00000002745_at"

 [] "ENSG00000002746_at"          "ENSG00000002822_at"

 [] "ENSG00000002834_at"          "ENSG00000002919_at"

 [] "ENSG00000002933_at"          "ENSG00000003056_at"

 [] "ENSG00000003096_at"          "ENSG00000003137_at"

 [] "ENSG00000003147_at"          "ENSG00000003249_at"

 [] "ENSG00000003393_at"          "ENSG00000003400_at"

从结果可以看出，hgu133plus2有54675个探针组，而hgu133plus2hsensgcdf只有20009个探针组，这是因为有些探针组被合并起来了，可能还有一些被舍弃掉。

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