> > #!/usr/bin/env Rscript > library(gage) Loading required package: graph Loading required package: multtest Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Warning message: '.readRDS' is deprecated. Use 'readRDS' instead. See help("Deprecated") > options(width=80) > Micro_array_data <- readExpData(file = "geo30195_expression_data_19_Jan_2012.gct", row.names = 1) > Gene_set <- readList("c1.all.v3.0.symbols.gmt") > Phenotype <- read.table(file = "geo30195_phenotype_19_Jan_2012_RAEB_vs_RA.cls", header = TRUE, sep = "\t", quote = "") > Col_names <- colnames(Phenotype) > Reference <- grep("RAEB",Col_names,ignore.case = F) > Target <- grep("ra",Col_names,ignore.case = F) > gstTest <- gage(exprs = Micro_array_data, gsets = Gene_set, ref = Reference, samp = Target, set.size = c(1,1000), same.dir = FALSE, + compare = "as.group", rank.test = TRUE, saaTest = gs.tTest) Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > # Samples of all the data files used > head(Micro_array_data) GSM747424 GSM747425 GSM747426 GSM747427 GSM747428 GSM747429 GSM747430 1007_s_at 756.8 1771.9 246.9 858.7 1895.7 300.0 570.4 1053_at 2092.3 2211.8 1005.2 2202.0 2439.5 1398.9 1308.2 117_at 267.1 128.6 81.4 162.4 205.7 242.2 723.6 121_at 1512.1 1181.5 1370.5 1541.1 1724.7 2199.6 1520.9 1255_g_at 96.5 96.8 130.0 17.6 117.0 20.6 63.6 1294_at 6083.3 2161.9 1981.8 6767.6 5200.9 1946.2 1404.7 GSM747431 GSM747432 GSM747433 GSM747434 GSM747435 GSM747436 GSM747437 1007_s_at 836.1 1782.7 922.0 488.8 2972.4 716.7 162.2 1053_at 1664.5 1418.9 2083.9 983.0 1629.6 1778.4 874.3 117_at 174.1 159.5 454.8 132.3 23.3 207.0 233.5 121_at 1676.2 1070.8 1539.5 1982.2 1438.2 1719.5 1256.4 1255_g_at 102.6 46.6 33.5 94.7 193.3 44.8 6.9 1294_at 3970.3 7292.7 2471.3 7187.6 10536.9 10906.3 2124.1 GSM747438 1007_s_at 1203.4 1053_at 1247.3 117_at 229.3 121_at 1758.9 1255_g_at 126.8 1294_at 8814.0 > head(Gene_set) $chr5q23 [1] "PTMAP2" "FTMT" "PRR16" "MGC32805" "MRPS5P3" "LOC402229" [7] "RPS17P2" "LOC728460" "GPX3" "GDF9" "LOX" "NRG2" [13] "EGR1" "ARGFXP1" "CDO1" "UBE2B" "RAD50" "NME5" [19] "DTWD2" "TNFAIP8" "SLC27A6" "CSNK1G3" "ADAMTS2" "CSF2" [25] "LOC389322" "LMNB1" "FLJ33630" "CTXN3" "SNX2" "ACTBP4" [31] "PRRC1" "GRAMD3" "COMMD10" "PPP2CA" "ZNF474" "LOC728342" [37] "SNX24" "ZNF608" "FBN2" "PGGT1B" "RNF14" "IL4" [43] "IL3" "IL5" "CAMLG" "SLC12A2" "LOC644659" "LOC644100" [49] "LOC644754" "ITGA2" "NEUROG1" "LOC728586" "FNIP1" "ANKRD43" [55] "Mar-03" "SEMA6A" "FLJ44606" "SRFBP1" "LOC348958" "PPIC" [61] "ADRA1B" "LOC728682" "IRF1" "HBEGF" "FABP6" "" [67] "" "" "" "" "" "" [73] "" "" "" "" "" "" [79] "" "" "" "" "" "" [85] "" "" "" "" "" "" [91] "" "" "" "" "" "" [97] "" "" "" "" "" "" [103] "" "" "" "" "" "" [109] "" "" "" "" "" "" [115] "" "" "" "" "" "" [121] "" "" "" "" "" "" [127] "" "" "" "" "" "" [133] "" "" "" "" "" "" [139] "" "" "" "" "" "" [145] "" "" "" "" "" "" [151] "" "" "" "" "" "" [157] "" "" "" "" "" "" [163] "" "" "" "" "" "" [169] "" "" "" "" "" "" [175] "" "" "" "" "" "" [181] "" "" "" "" "" "" [187] "" "" "" "" "" "" [193] "" "" "" "" "" "" [199] "" "" "" "" "" "" [205] "" "" "" "" "" "" [211] "" "" "" "" "" "" [217] "" "" "" "" "" "" [223] "" "" "" "" "" "" [229] "" "" "" "" "" "" [235] "" "" "" "" "" "" [241] "" "" "" "" "" "" [247] "" "" "" "" "" "" [253] "" "" "" "" "" "" [259] "" "" "" "" "" "" [265] "" "" "" "" "" "" [271] "" "" "" "" "" "" [277] "" "" "" "" "" "" [283] "" "" "" "" "" "" [289] "" "" "" "" "" "" [295] "" "" "" "" "" "" [301] "" "" "" "" "" "" [307] "" "" "" "" "" "" [313] "" "" "" "" "" "" [319] "" "" "" "" "" "" [325] "" "" "" "" "" "" [331] "" "" "" "" "" "" [337] "" "" "" "" "" "" [343] "" "" "" "" "" "" [349] "" "" "" "" "" "" [355] "" "" "" "" "" "" [361] "" "" "" "" "" "" [367] "" "" "" "" "" "" [373] "" "" "" "" "" "" [379] "" "" "" "" "" "" [385] "" "" "" "" "" "" [391] "" "" "" "" "" "" [397] "" "" "" "" "" "" [403] "" "" "" "" "" "" [409] "" "" "" "" "" "" [415] "" "" "" "" "" "" [421] "" "" "" "" "" "" [427] "" "" "" "" "" "" [433] "" "" "" "" "" "" [439] "" "" "" "" "" "" [445] "" "" "" "" "" "" [451] "" "" "" "" "" "" [457] "" "" "" "" "" "" [463] "" "" "" "" "" "" [469] "" "" "" "" "" "" [475] "" "" "" "" "" "" [481] "" "" "" "" "" "" [487] "" "" "" "" "" "" [493] "" "" "" "" "" "" [499] "" "" "" "" "" "" [505] "" "" "" "" "" "" [511] "" "" "" "" "" "" [517] "" "" "" "" "" "" [523] "" "" "" "" "" "" [529] "" "" "" "" "" "" [535] "" "" "" "" "" "" [541] "" "" "" "" "" "" [547] "" "" "" "" "" "" [553] "" "" "" "" "" "" [559] "" "" "" "" "" "" [565] "" "" "" "" "" "" [571] "" "" "" "" "" "" [577] "" "" "" "" "" "" [583] "" "" "" "" "" "" [589] "" "" "" "" "" "" [595] "" "" "" "" "" "" [601] "" "" "" "" "" "" [607] "" "" "" "" "" "" [613] "" "" "" "" "" "" [619] "" "" "" "" "" "" [625] "" "" "" "" "" "" [631] "" "" "" "" "" "" [637] "" "" "" "" "" "" [643] "" "" "" "" "" "" [649] "" "" "" "" "" "" [655] "" "" "" "" "" "" [661] "" "" "" "" "" "" [667] "" "" "" "" "" "" [673] "" "" "" "" "" "" [679] "" "" "" "" "" "" [685] "" "" "" "" "" "" [691] "" "" "" "" "" "" [697] "" "" "" "" "" "" [703] "" "" "" "" "" "" [709] "" "" "" "" "" "" [715] "" "" "" "" "" "" [721] "" "" "" "" "" "" [727] "" "" "" "" "" "" [733] "" "" "" "" "" "" [739] "" "" "" "" "" "" [745] "" "" "" "" "" "" [751] "" "" "" "" "" "" [757] "" "" "" "" "" "" [763] "" "" "" "" "" "" [769] "" "" "" "" "" "" [775] "" "" "" "" "" "" [781] "" "" "" "" $chr16q24 [1] "LOC642452" "SNORD68" "RPL13" "TRAPPC2L" "C16ORF74" "SLC7A5" [7] "COX4NB" "FAM92B" "ZNF778" "MC1R" "TMEM148" "LOC283861" [13] "FOXF1" "LOC401864" "LRRC50" "LOC400553" "SPIRE2" "PRDM7" [19] "LOC400548" "WFDC1" "FAM38A" "DBNDD1" "MVD" "CA5A" [25] "IL17C" "FLJ45121" "RNF166" "GALNS" "KIAA1609" "C16ORF7" [31] "LOC728054" "TCF25" "C16ORF3" "GINS2" "C16ORF81" "CPNE7" [37] "MTHFSD" "LOC197331" "GAS8" "AFG3L1" "FLJ40448" "LOC146429" [43] "FLJ46320" "LOC728028" "PLCG2" "VV" "FBXO31" "HDLC3" [49] "LOC283904" "TAF1C" "LOC729887" "SPG7" "JPH3" "LOC729519" [55] "LOC146513" "CBFA2T3" "CDT1" "FLJ34515" "LOC123862" "MAP1LC3B" [61] "ANKRD11" "CDK10" "FLJ30679" "LOC648774" "KCNG4" "FANCA" [67] "DPEP1" "TUBB3" "LOC727710" "KIAA0182" "LOC642533" "GAN" [73] "BANP" "KLHDC4" "ZCCHC14" "LOC123855" "KIAA0513" "ZFPM1" [79] "C16ORF55" "ZNF276" "ZNF469" "HSD17B2" "LOC400558" "CRISPLD2" [85] "FEOM3" "LOC654780" "FOXL1" "COTL1" "MGC23284" "APRT" [91] "CYBA" "CDH13" "SNAI3" "CDH15" "HSDL1" "IRF8" [97] "MBTPS1" "" "" "" "" "" [103] "" "" "" "" "" "" [109] "" "" "" "" "" "" [115] "" "" "" "" "" "" [121] "" "" "" "" "" "" [127] "" "" "" "" "" "" [133] "" "" "" "" "" "" [139] "" "" "" "" "" "" [145] "" "" "" "" "" "" [151] "" "" "" "" "" "" [157] "" "" "" "" "" "" [163] "" "" "" "" "" "" [169] "" "" "" "" "" "" [175] "" "" "" "" "" "" [181] "" "" "" "" "" "" [187] "" "" "" "" "" "" [193] "" "" "" "" "" "" [199] "" "" "" "" "" "" [205] "" "" "" "" "" "" [211] "" "" "" "" "" "" [217] "" "" "" "" "" "" [223] "" "" "" "" "" "" [229] "" "" "" "" "" "" [235] "" "" "" "" "" "" [241] "" "" "" "" "" "" [247] "" "" "" "" "" "" [253] "" "" "" "" "" "" [259] "" "" "" "" "" "" [265] "" "" "" "" "" "" [271] "" "" "" "" "" "" [277] "" "" "" "" "" "" [283] "" "" "" "" "" "" [289] "" "" "" "" "" "" [295] "" "" "" "" "" "" [301] "" "" "" "" "" "" [307] "" "" "" "" "" "" [313] "" "" "" "" "" "" [319] "" "" "" "" "" "" [325] "" "" "" "" "" "" [331] "" "" "" "" "" "" [337] "" "" "" "" "" "" [343] "" "" "" "" "" "" [349] "" "" "" "" "" "" [355] "" "" "" "" "" "" [361] "" "" "" "" "" "" [367] "" "" "" "" "" "" [373] "" "" "" "" "" "" [379] "" "" "" "" "" "" [385] "" "" "" "" "" "" [391] "" "" "" "" "" "" [397] "" "" "" "" "" "" [403] "" "" "" "" "" "" [409] "" "" "" "" "" "" [415] "" "" "" "" "" "" [421] "" "" "" "" "" "" [427] "" "" "" "" "" "" [433] "" "" "" "" "" "" [439] "" "" "" "" "" "" [445] "" "" "" "" "" "" [451] "" "" "" "" "" "" [457] "" "" "" "" "" "" [463] "" "" "" "" "" "" [469] "" "" "" "" "" "" [475] "" "" "" "" "" "" [481] "" "" "" "" "" "" [487] "" "" "" "" "" "" [493] "" "" "" "" "" "" [499] "" "" "" "" "" "" [505] "" "" "" "" "" "" [511] "" "" "" "" "" "" [517] "" "" "" "" "" "" [523] "" "" "" "" "" "" [529] "" "" "" "" "" "" [535] "" "" "" "" "" "" [541] "" "" "" "" "" "" [547] "" "" "" "" "" "" [553] "" "" "" "" "" "" [559] "" "" "" "" "" "" [565] "" "" "" "" "" "" [571] "" "" "" "" "" "" [577] "" "" "" "" "" "" [583] "" "" "" "" "" "" [589] "" "" "" "" "" "" [595] "" "" "" "" "" "" [601] "" "" "" "" "" "" [607] "" "" "" "" "" "" [613] "" "" "" "" "" "" [619] "" "" "" "" "" "" [625] "" "" "" "" "" "" [631] "" "" "" "" "" "" [637] "" "" "" "" "" "" [643] "" "" "" "" "" "" [649] "" "" "" "" "" "" [655] "" "" "" "" "" "" [661] "" "" "" "" "" "" [667] "" "" "" "" "" "" [673] "" "" "" "" "" "" [679] "" "" "" "" "" "" [685] "" "" "" "" "" "" [691] "" "" "" "" "" "" [697] "" "" "" "" "" "" [703] "" "" "" "" "" "" [709] "" "" "" "" "" "" [715] "" "" "" "" "" "" [721] "" "" "" "" "" "" [727] "" "" "" "" "" "" [733] "" "" "" "" "" "" [739] "" "" "" "" "" "" [745] "" "" "" "" "" "" [751] "" "" "" "" "" "" [757] "" "" "" "" "" "" [763] "" "" "" "" "" "" [769] "" "" "" "" "" "" [775] "" "" "" "" "" "" [781] "" "" "" "" $chr8q24 [1] "LYPD2" "KIFC2" "EIF2C2" "ADCY8" "ZNF250" "MAF1" [7] "FLJ45872" "ZNF251" "TSNARE1" "MLVI4" "ZNF252" "NOV" [13] "ST3GAL1" "KCNK9" "RAD21" "FAM49B" "OPLAH" "LOC728724" [19] "LOC401480" "TIGD5" "SCRT1" "TSSK5P2" "CYHR1" "DEPDC6" [25] "TSSK5P1" "ARC" "LRRC6" "LOC286109" "COL22A1" "ZHX2" [31] "C8ORF55" "SPATC1" "C8ORF54" "ZNF7" "PARP10" "TATDN1" [37] "LOC286052" "C8ORF51" "CHRAC1" "LYNX1" "FER1L5" "TRMT12" [43] "KIAA1875" "RNF139" "HHLA1" "PSCA" "HAS2" "FBXL6" [49] "EXT1" "NRBP2" "ZC3H3" "AK3P2" "CYCSP23" "DERL1" [55] "ZNF517" "RHPN1" "ENPP2" "LOC642574" "BOP1" "LOC442396" [61] "SCRIB" "C8ORF24" "JRK" "FOXH1" "C8ORF26" "ZNF696" [67] "PPP1R16A" "RPL8" "BAI1" "NDRG1" "GML" "GPR20" [73] "SLC30A8" "TAF2" "RECQL4" "PVT1" "ZNF623" "CCDC26" [79] "FAM10A6" "ATAD2" "C8ORF33" "C8ORF31" "NFKBIL2" "HPV18I1" [85] "WDR67" "GRINA" "FBXO32" "MAFA" "FAM84B" "FAM91A1" [91] "SLURP1" "SLC45A4" "ZFP41" "CYC1" "ZNF16" "LRRC14" [97] "GPR172A" "TNFRSF11B" "FAM83A" "KCNQ3" "WISP1" "GLI4" [103] "HSF1" "C8ORF30B" "C8ORF30A" "SHARPIN" "MTBP" "NSMCE2" [109] "FAM83H" "MYC" "ADCK5" "NAPRT1" "KHDRBS3" "THMA" [115] "LOC286094" "MRPS36P3" "EXOSC4" "TMEM71" "C8ORF17" "TOP1MT" [121] "TMEM75" "LRRC24" "LOC157381" "TMEM65" "DGAT1" "SQLE" [127] "EEF1D" "DENND3" "FRA8E" "FRA8D" "CPSF1" "FRA8C" [133] "C8ORF60" "TG" "PYCRL" "C8ORFK29" "C8ORF63" "MFSD3" [139] "NDUFB9" "C8ORF66" "KIAA0196" "GPAA1" "ZNF34" "LOC392266" [145] "LOC392264" "LOC392265" "LY6D" "LY6E" "ZNF707" "LY6H" [151] "BVR1" "LOC727967" "TSTA3" "PHF20L1" "SLC39A4" "ECA1" [157] "LOC392268" "C8ORF73" "LOC286123" "LOC286121" "HHCM" "C8ORF77" [163] "SAMD12" "SCXA" "EPPK1" "LOC441383" "C8ORF78" "LOC286126" [169] "C8ORF76" "SCXB" "LY6K" "LOC650095" "OC90" "FLJ43860" [175] "LOC392275" "PTP4A3" "MAPK15" "ANXA13" "GPT" "VPS28" [181] "LOC727872" "ZNF572" "" "" "" "" [187] "" "" "" "" "" "" [193] "" "" "" "" "" "" [199] "" "" "" "" "" "" [205] "" "" "" "" "" "" [211] "" "" "" "" "" "" [217] "" "" "" "" "" "" [223] "" "" "" "" "" "" [229] "" "" "" "" "" "" [235] "" "" "" "" "" "" [241] "" "" "" "" "" "" [247] "" "" "" "" "" "" [253] "" "" "" "" "" "" [259] "" "" "" "" "" "" [265] "" "" "" "" "" "" [271] "" "" "" "" "" "" [277] "" "" "" "" "" "" [283] "" "" "" "" "" "" [289] "" "" "" "" "" "" [295] "" "" "" "" "" "" [301] "" "" "" "" "" "" [307] "" "" "" "" "" "" [313] "" "" "" "" "" "" [319] "" "" "" "" "" "" [325] "" "" "" "" "" "" [331] "" "" "" "" "" "" [337] "" "" "" "" "" "" [343] "" "" "" "" "" "" [349] "" "" "" "" "" "" [355] "" "" "" "" "" "" [361] "" "" "" "" "" "" [367] "" "" "" "" "" "" [373] "" "" "" "" "" "" [379] "" "" "" "" "" "" [385] "" "" "" "" "" "" [391] "" "" "" "" "" "" [397] "" "" "" "" "" "" [403] "" "" "" "" "" "" [409] "" "" "" "" "" "" [415] "" "" "" "" "" "" [421] "" "" "" "" "" "" [427] "" "" "" "" "" "" [433] "" "" "" "" "" "" [439] "" "" "" "" "" "" [445] "" "" "" "" "" "" [451] "" "" "" "" "" "" [457] "" "" "" "" "" "" [463] "" "" "" "" "" "" [469] "" "" "" "" "" "" [475] "" "" "" "" "" "" [481] "" "" "" "" "" "" [487] "" "" "" "" "" "" [493] "" "" "" "" "" "" [499] "" "" "" "" "" "" [505] "" "" "" "" "" "" [511] "" "" "" "" "" "" [517] "" "" "" "" "" "" [523] "" "" "" "" "" "" [529] "" "" "" "" "" "" [535] "" "" "" "" "" "" [541] "" "" "" "" "" "" [547] "" "" "" "" "" "" [553] "" "" "" "" "" "" [559] "" "" "" "" "" "" [565] "" "" "" "" "" "" [571] "" "" "" "" "" "" [577] "" "" "" "" "" "" [583] "" "" "" "" "" "" [589] "" "" "" "" "" "" [595] "" "" "" "" "" "" [601] "" "" "" "" "" "" [607] "" "" "" "" "" "" [613] "" "" "" "" "" "" [619] "" "" "" "" "" "" [625] "" "" "" "" "" "" [631] "" "" "" "" "" "" [637] "" "" "" "" "" "" [643] "" "" "" "" "" "" [649] "" "" "" "" "" "" [655] "" "" "" "" "" "" [661] "" "" "" "" "" "" [667] "" "" "" "" "" "" [673] "" "" "" "" "" "" [679] "" "" "" "" "" "" [685] "" "" "" "" "" "" [691] "" "" "" "" "" "" [697] "" "" "" "" "" "" [703] "" "" "" "" "" "" [709] "" "" "" "" "" "" [715] "" "" "" "" "" "" [721] "" "" "" "" "" "" [727] "" "" "" "" "" "" [733] "" "" "" "" "" "" [739] "" "" "" "" "" "" [745] "" "" "" "" "" "" [751] "" "" "" "" "" "" [757] "" "" "" "" "" "" [763] "" "" "" "" "" "" [769] "" "" "" "" "" "" [775] "" "" "" "" "" "" [781] "" "" "" "" $chr13q11 [1] "LOC645626" "ZMYM2" "FGF9" "XPO4" [5] "LOC729524" "SACS" "LOC729535" "ATP12A" [9] "DKFZP686A1627" "LOC729501" "LATS2" "LOC654337" [13] "GJB2" "IL17D" "CRYL1" "PSPC1" [17] "LOC283523" "PARP4" "" "" [21] "" "" "" "" [25] "" "" "" "" [29] "" "" "" "" [33] "" "" "" "" [37] "" "" "" "" [41] "" "" "" "" [45] "" "" "" "" [49] "" "" "" "" [53] "" "" "" "" [57] "" "" "" "" [61] "" "" "" "" [65] "" "" "" "" [69] "" "" "" "" [73] "" "" "" "" [77] "" "" "" "" [81] "" "" "" "" [85] "" "" "" "" [89] "" "" "" "" [93] "" "" "" "" [97] "" "" "" "" [101] "" "" "" "" [105] "" "" "" "" [109] "" "" "" "" [113] "" "" "" "" [117] "" "" "" "" [121] "" "" "" "" [125] "" "" "" "" [129] "" "" "" "" [133] "" "" "" "" [137] "" "" "" "" [141] "" "" "" "" [145] "" "" "" "" [149] "" "" "" "" [153] "" "" "" "" [157] "" "" "" "" [161] "" "" "" "" [165] "" "" "" "" [169] "" "" "" "" [173] "" "" "" "" [177] "" "" "" "" [181] "" "" "" "" [185] "" "" "" "" [189] "" "" "" "" [193] "" "" "" "" [197] "" "" "" "" [201] "" "" "" "" [205] "" "" "" "" [209] "" "" "" "" [213] "" "" "" "" [217] "" "" "" "" [221] "" "" "" "" [225] "" "" "" "" [229] "" "" "" "" [233] "" "" "" "" [237] "" "" "" "" [241] "" "" "" "" [245] "" "" "" "" [249] "" "" "" "" [253] "" "" "" "" [257] "" "" "" "" [261] "" "" "" "" [265] "" "" "" "" [269] "" "" "" "" [273] "" "" "" "" [277] "" "" "" "" [281] "" "" "" "" [285] "" "" "" "" [289] "" "" "" "" [293] "" "" "" "" [297] "" "" "" "" [301] "" "" "" "" [305] "" "" "" "" [309] "" "" "" "" [313] "" "" "" "" [317] "" "" "" "" [321] "" "" "" "" [325] "" "" "" "" [329] "" "" "" "" [333] "" "" "" "" [337] "" "" "" "" [341] "" "" "" "" [345] "" "" "" "" [349] "" "" "" "" [353] "" "" "" "" [357] "" "" "" "" [361] "" "" "" "" [365] "" "" "" "" [369] "" "" "" "" [373] "" "" "" "" [377] "" "" "" "" [381] "" "" "" "" [385] "" "" "" "" [389] "" "" "" "" [393] "" "" "" "" [397] "" "" "" "" [401] "" "" "" "" [405] "" "" "" "" [409] "" "" "" "" [413] "" "" "" "" [417] "" "" "" "" [421] "" "" "" "" [425] "" "" "" "" [429] "" "" "" "" [433] "" "" "" "" [437] "" "" "" "" [441] "" "" "" "" [445] "" "" "" "" [449] "" "" "" "" [453] "" "" "" "" [457] "" "" "" "" [461] "" "" "" "" [465] "" "" "" "" [469] "" "" "" "" [473] "" "" "" "" [477] "" "" "" "" [481] "" "" "" "" [485] "" "" "" "" [489] "" "" "" "" [493] "" "" "" "" [497] "" "" "" "" [501] "" "" "" "" [505] "" "" "" "" [509] "" "" "" "" [513] "" "" "" "" [517] "" "" "" "" [521] "" "" "" "" [525] "" "" "" "" [529] "" "" "" "" [533] "" "" "" "" [537] "" "" "" "" [541] "" "" "" "" [545] "" "" "" "" [549] "" "" "" "" [553] "" "" "" "" [557] "" "" "" "" [561] "" "" "" "" [565] "" "" "" "" [569] "" "" "" "" [573] "" "" "" "" [577] "" "" "" "" [581] "" "" "" "" [585] "" "" "" "" [589] "" "" "" "" [593] "" "" "" "" [597] "" "" "" "" [601] "" "" "" "" [605] "" "" "" "" [609] "" "" "" "" [613] "" "" "" "" [617] "" "" "" "" [621] "" "" "" "" [625] "" "" "" "" [629] "" "" "" "" [633] "" "" "" "" [637] "" "" "" "" [641] "" "" "" "" [645] "" "" "" "" [649] "" "" "" "" [653] "" "" "" "" [657] "" "" "" "" [661] "" "" "" "" [665] "" "" "" "" [669] "" "" "" "" [673] "" "" "" "" [677] "" "" "" "" [681] "" "" "" "" [685] "" "" "" "" [689] "" "" "" "" [693] "" "" "" "" [697] "" "" "" "" [701] "" "" "" "" [705] "" "" "" "" [709] "" "" "" "" [713] "" "" "" "" [717] "" "" "" "" [721] "" "" "" "" [725] "" "" "" "" [729] "" "" "" "" [733] "" "" "" "" [737] "" "" "" "" [741] "" "" "" "" [745] "" "" "" "" [749] "" "" "" "" [753] "" "" "" "" [757] "" "" "" "" [761] "" "" "" "" [765] "" "" "" "" [769] "" "" "" "" [773] "" "" "" "" [777] "" "" "" "" [781] "" "" "" "" $chr7p21 [1] "DNAH11" "LOC221814" "MYL7" "CRS" "TAS2R2" "RAD17P1" [7] "ZNF12" "CBX3" "COL28A1" "PSPH" "SCA21" "BZW2" [13] "FERD3L" "TSC22D4" "PDE1C" "SOSTDC1" "PER4" "PRPS1L1" [19] "LOC340268" "C1GALT1" "LOC317727" "TWIST1" "NDUFA4" "MDDC" [25] "LOC541472" "IL6" "GAPDHL13" "LOC729852" "ANKMY2" "CYCS" [31] "TSPAN13" "LOC389465" "TMEM106B" "CRHR2" "NPVF" "NPM1P11" [37] "PLEKHA8" "PHF14" "NPM1P13" "SCIN" "LOC441198" "SP8" [43] "AGR2" "SNX13" "ARL4A" "" "" "" [49] "" "" "" "" "" "" [55] "" "" "" "" "" "" [61] "" "" "" "" "" "" [67] "" "" "" "" "" "" [73] "" "" "" "" "" "" [79] "" "" "" "" "" "" [85] "" "" "" "" "" "" [91] "" "" "" "" "" "" [97] "" "" "" "" "" "" [103] "" "" "" "" "" "" [109] "" "" "" "" "" "" [115] "" "" "" "" "" "" [121] "" "" "" "" "" "" [127] "" "" "" "" "" "" [133] "" "" "" "" "" "" [139] "" "" "" "" "" "" [145] "" "" "" "" "" "" [151] "" "" "" "" "" "" [157] "" "" "" "" "" "" [163] "" "" "" "" "" "" [169] "" "" "" "" "" "" [175] "" "" "" "" "" "" [181] "" "" "" "" "" "" [187] "" "" "" "" "" "" [193] "" "" "" "" "" "" [199] "" "" "" "" "" "" [205] "" "" "" "" "" "" [211] "" "" "" "" "" "" [217] "" "" "" "" "" "" [223] "" "" "" "" "" "" [229] "" "" "" "" "" "" [235] "" "" "" "" "" "" [241] "" "" "" "" "" "" [247] "" "" "" "" "" "" [253] "" "" "" "" "" "" [259] "" "" "" "" "" "" [265] "" "" "" "" "" "" [271] "" "" "" "" "" "" [277] "" "" "" "" "" "" [283] "" "" "" "" "" "" [289] "" "" "" "" "" "" [295] "" "" "" "" "" "" [301] "" "" "" "" "" "" [307] "" "" "" "" "" "" [313] "" "" "" "" "" "" [319] "" "" "" "" "" "" [325] "" "" "" "" "" "" [331] "" "" "" "" "" "" [337] "" "" "" "" "" "" [343] "" "" "" "" "" "" [349] "" "" "" "" "" "" [355] "" "" "" "" "" "" [361] "" "" "" "" "" "" [367] "" "" "" "" "" "" [373] "" "" "" "" "" "" [379] "" "" "" "" "" "" [385] "" "" "" "" "" "" [391] "" "" "" "" "" "" [397] "" "" "" "" "" "" [403] "" "" "" "" "" "" [409] "" "" "" "" "" "" [415] "" "" "" "" "" "" [421] "" "" "" "" "" "" [427] "" "" "" "" "" "" [433] "" "" "" "" "" "" [439] "" "" "" "" "" "" [445] "" "" "" "" "" "" [451] "" "" "" "" "" "" [457] "" "" "" "" "" "" [463] "" "" "" "" "" "" [469] "" "" "" "" "" "" [475] "" "" "" "" "" "" [481] "" "" "" "" "" "" [487] "" "" "" "" "" "" [493] "" "" "" "" "" "" [499] "" "" "" "" "" "" [505] "" "" "" "" "" "" [511] "" "" "" "" "" "" [517] "" "" "" "" "" "" [523] "" "" "" "" "" "" [529] "" "" "" "" "" "" [535] "" "" "" "" "" "" [541] "" "" "" "" "" "" [547] "" "" "" "" "" "" [553] "" "" "" "" "" "" [559] "" "" "" "" "" "" [565] "" "" "" "" "" "" [571] "" "" "" "" "" "" [577] "" "" "" "" "" "" [583] "" "" "" "" "" "" [589] "" "" "" "" "" "" [595] "" "" "" "" "" "" [601] "" "" "" "" "" "" [607] "" "" "" "" "" "" [613] "" "" "" "" "" "" [619] "" "" "" "" "" "" [625] "" "" "" "" "" "" [631] "" "" "" "" "" "" [637] "" "" "" "" "" "" [643] "" "" "" "" "" "" [649] "" "" "" "" "" "" [655] "" "" "" "" "" "" [661] "" "" "" "" "" "" [667] "" "" "" "" "" "" [673] "" "" "" "" "" "" [679] "" "" "" "" "" "" [685] "" "" "" "" "" "" [691] "" "" "" "" "" "" [697] "" "" "" "" "" "" [703] "" "" "" "" "" "" [709] "" "" "" "" "" "" [715] "" "" "" "" "" "" [721] "" "" "" "" "" "" [727] "" "" "" "" "" "" [733] "" "" "" "" "" "" [739] "" "" "" "" "" "" [745] "" "" "" "" "" "" [751] "" "" "" "" "" "" [757] "" "" "" "" "" "" [763] "" "" "" "" "" "" [769] "" "" "" "" "" "" [775] "" "" "" "" "" "" [781] "" "" "" "" $chr10q23 [1] "SNCG" "LOC389997" "UFS" "IDE" "GPR120" "PDLIM1" [7] "ANKRD1" "SMNDC1" "MMRN2" "RCM2" "GHITM" "TBC1D12" [13] "DNTT" "TMEM20" "CH25H" "RPP30" "EIF2S2P3" "RGR" [19] "POLL" "C10ORF100" "FLJ37201" "CYP26A1" "C10ORF99" "LOC728218" [25] "LOC283014" "TNKS2" "CTSLL1" "MRPL50P4" "HHEX" "PLCE1" [31] "LOC643768" "RPL7AP8" "RBP4" "FAM22D" "LOC119358" "NOC3L" [37] "SORCS1" "FLJ34077" "FRA10A" "LOC728190" "SORCS3" "PPP1R3C" [43] "DUSP13" "ENTPD7" "STAMBPL1" "HECTD2" "ENTPD1" "FAM22A" [49] "HELLS" "BLNK" "SCD" "WAPAL" "LOC387703" "ATAD1" [55] "LOC642666" "NMSR" "LOC219347" "LOC728027" "LOC389990" "TLL2" [61] "SPG9" "CPEB3" "CDB2" "NUDT9P1" "SLC16A12" "HPS1" [67] "PTEN" "LOC170425" "LOC399804" "SH2D4B" "PCGF5" "FRAT2" [73] "LOC728558" "DLG5" "LOC439994" "KIAA0894" "LOC643529" "MINPP1" [79] "C10ORF57" "C10ORF58" "FAM35A" "LOC677759" "SLIT1" "CFLP1" [85] "ARL3" "PANK1" "ANKRD22" "LOC642934" "NDUFB8" "C10ORF116" [91] "LOC647532" "SORBS1" "HPSE2" "DFNB57" "EXOC6" "DYDC2" [97] "CNNM2" "LIPA" "SRP9L1" "TSPAN14" "C10ORF129" "Mar-05" [103] "LOC474358" "PLAC9" "CNNM1" "IFIT3" "IFIT2" "CYP26C1" [109] "IFIT5" "LOC728475" "LIPF" "" "" "" [115] "" "" "" "" "" "" [121] "" "" "" "" "" "" [127] "" "" "" "" "" "" [133] "" "" "" "" "" "" [139] "" "" "" "" "" "" [145] "" "" "" "" "" "" [151] "" "" "" "" "" "" [157] "" "" "" "" "" "" [163] "" "" "" "" "" "" [169] "" "" "" "" "" "" [175] "" "" "" "" "" "" [181] "" "" "" "" "" "" [187] "" "" "" "" "" "" [193] "" "" "" "" "" "" [199] "" "" "" "" "" "" [205] "" "" "" "" "" "" [211] "" "" "" "" "" "" [217] "" "" "" "" "" "" [223] "" "" "" "" "" "" [229] "" "" "" "" "" "" [235] "" "" "" "" "" "" [241] "" "" "" "" "" "" [247] "" "" "" "" "" "" [253] "" "" "" "" "" "" [259] "" "" "" "" "" "" [265] "" "" "" "" "" "" [271] "" "" "" "" "" "" [277] "" "" "" "" "" "" [283] "" "" "" "" "" "" [289] "" "" "" "" "" "" [295] "" "" "" "" "" "" [301] "" "" "" "" "" "" [307] "" "" "" "" "" "" [313] "" "" "" "" "" "" [319] "" "" "" "" "" "" [325] "" "" "" "" "" "" [331] "" "" "" "" "" "" [337] "" "" "" "" "" "" [343] "" "" "" "" "" "" [349] "" "" "" "" "" "" [355] "" "" "" "" "" "" [361] "" "" "" "" "" "" [367] "" "" "" "" "" "" [373] "" "" "" "" "" "" [379] "" "" "" "" "" "" [385] "" "" "" "" "" "" [391] "" "" "" "" "" "" [397] "" "" "" "" "" "" [403] "" "" "" "" "" "" [409] "" "" "" "" "" "" [415] "" "" "" "" "" "" [421] "" "" "" "" "" "" [427] "" "" "" "" "" "" [433] "" "" "" "" "" "" [439] "" "" "" "" "" "" [445] "" "" "" "" "" "" [451] "" "" "" "" "" "" [457] "" "" "" "" "" "" [463] "" "" "" "" "" "" [469] "" "" "" "" "" "" [475] "" "" "" "" "" "" [481] "" "" "" "" "" "" [487] "" "" "" "" "" "" [493] "" "" "" "" "" "" [499] "" "" "" "" "" "" [505] "" "" "" "" "" "" [511] "" "" "" "" "" "" [517] "" "" "" "" "" "" [523] "" "" "" "" "" "" [529] "" "" "" "" "" "" [535] "" "" "" "" "" "" [541] "" "" "" "" "" "" [547] "" "" "" "" "" "" [553] "" "" "" "" "" "" [559] "" "" "" "" "" "" [565] "" "" "" "" "" "" [571] "" "" "" "" "" "" [577] "" "" "" "" "" "" [583] "" "" "" "" "" "" [589] "" "" "" "" "" "" [595] "" "" "" "" "" "" [601] "" "" "" "" "" "" [607] "" "" "" "" "" "" [613] "" "" "" "" "" "" [619] "" "" "" "" "" "" [625] "" "" "" "" "" "" [631] "" "" "" "" "" "" [637] "" "" "" "" "" "" [643] "" "" "" "" "" "" [649] "" "" "" "" "" "" [655] "" "" "" "" "" "" [661] "" "" "" "" "" "" [667] "" "" "" "" "" "" [673] "" "" "" "" "" "" [679] "" "" "" "" "" "" [685] "" "" "" "" "" "" [691] "" "" "" "" "" "" [697] "" "" "" "" "" "" [703] "" "" "" "" "" "" [709] "" "" "" "" "" "" [715] "" "" "" "" "" "" [721] "" "" "" "" "" "" [727] "" "" "" "" "" "" [733] "" "" "" "" "" "" [739] "" "" "" "" "" "" [745] "" "" "" "" "" "" [751] "" "" "" "" "" "" [757] "" "" "" "" "" "" [763] "" "" "" "" "" "" [769] "" "" "" "" "" "" [775] "" "" "" "" "" "" [781] "" "" "" "" > head(Phenotype) [1] ra ra.1 RAEB ra.2 ra.3 RAEB.1 RAEB.2 ra.4 RAEB.3 ra.5 [11] RAEB.4 RAEB.5 ra.6 RAEB.6 RAEB.7 <0 rows> (or 0-length row.names) > print(Reference) [1] 3 6 7 9 11 12 14 15 > print(Target) [1] 1 2 4 5 8 10 13 >