#PUNTO EPECIAL, GENÓMICA EN BIOMARCADORES#
#2.11. UNA BASE DE DATOS DE EXPRESIÓN GENÓMICA EN CÁNCER DE PULMÓN DE CÉLULAS NO PEQUÑAS, DE ACEURDO CON DOS TRATAMIENTOS: UNO RESISTENTE Y UNO SENSIBLE. MOSTRANDO QUE CON EL TRATMIENTO PARA EL CUAL EL CÁNCER DE PULMÓN EN MENCIÓN ES SENSIBLE, HAY EXPRESIÓN EN BAJA DE ALGUNOS GENES Y EXPRESIÓN EN BAJA DE OTROS GENES RELACIONADOS CON LA APOPTOSIS TUMORAL. ES UNA BREVE EXPLICACIÓN AL RESPECTO DE UNA DE LAS BASES DE DATOS.
# Version info: R 4.2.2, Biobase 2.58.0, GEOquery 2.66.0, limma 3.54.0
################################################################
# load series and platform data from GEO
library(GEOquery)
## Loading required package: Biobase
## Loading required package: BiocGenerics
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
## table, tapply, union, unique, unsplit, which.max, which.min
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
## Setting options('download.file.method.GEOquery'='auto')
## Setting options('GEOquery.inmemory.gpl'=FALSE)
library(limma)
##
## Attaching package: 'limma'
## The following object is masked from 'package:BiocGenerics':
##
## plotMA
library(umap)
gset <- getGEO("GSE221334", GSEMatrix =TRUE, AnnotGPL=FALSE)
## Found 1 file(s)
## GSE221334_series_matrix.txt.gz
if (length(gset) > 1) idx <- grep("GPL19956", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
# make proper column names to match toptable
fvarLabels(gset) <- make.names(fvarLabels(gset))
# group membership for all samples
gsms <- "00X11XXXXXXX"
sml <- strsplit(gsms, split="")[[1]]
# filter out excluded samples (marked as "X")
sel <- which(sml != "X")
sml <- sml[sel]
gset <- gset[ ,sel]
# log2 transformation
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
(qx[6]-qx[1] > 50 && qx[2] > 0)
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }
# assign samples to groups and set up design matrix
gs <- factor(sml)
groups <- make.names(c("tto1","tto2"))
levels(gs) <- groups
gset$group <- gs
design <- model.matrix(~group + 0, gset)
colnames(design) <- levels(gs)
gset <- gset[complete.cases(exprs(gset)), ] # skip missing values
fit <- lmFit(gset, design) # fit linear model
# set up contrasts of interest and recalculate model coefficients
cts <- paste(groups[1], groups[2], sep="-")
cont.matrix <- makeContrasts(contrasts=cts, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
# compute statistics and table of top significant genes
fit2 <- eBayes(fit2, 0.01)
## Warning: Zero sample variances detected, have been offset away from zero
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)
tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","GB_ACC","SPOT_ID"))
write.table(tT, file=stdout(), row.names=F, sep="\t")
## "ID" "adj.P.Val" "P.Value" "t" "B" "logFC" "GB_ACC" "SPOT_ID"
## "IBSP" 0.0284378147311482 7.2545445742725e-05 -34.5748634150912 2.30837537265909 -3.0797478806074 "NM_004967.3" ""
## "RAC2" 0.0284378147311482 7.2545445742725e-05 -34.5748634150912 2.30837537265909 -3.0797478806074 "NM_002872.3" ""
## "EYA1" 0.156315759646222 0.000766245113955456 15.2025519950692 0.638467742438322 0.80971766426229 "NM_172059.2" ""
## "NEG_F" 0.156315759646222 0.000797529385950111 -14.9908959267622 0.599778316595135 -0.58595642709711 "" "ERCC_00126.1"
## "CALML6" 0.209664130751946 0.00140657879153786 -12.282372664845 0.021259937231239 -3.65198548220662 "NM_138705.2" ""
## "GRB2" 0.209664130751946 0.00222480178490143 -10.4465824757983 -0.481766181100058 -0.392411013862249 "NM_002086.4" ""
## "COL4A3" 0.209664130751946 0.00255060730904196 -9.95254060237299 -0.636831047526385 -1.22557626840689 "NM_000091.3" ""
## "CDC25A" 0.209664130751946 0.00288532469300679 9.5260082434113 -0.778521864845107 0.387245842202834 "NM_001789.2" ""
## "NKD1" 0.209664130751946 0.00375659105729381 8.67081221499593 -1.08688493219524 0.353443749334671 "NM_033119.3" ""
## "RET" 0.209664130751946 0.00413831438804682 -8.37573636411537 -1.20157219621158 -0.78134590471281 "NM_020630.4" ""
## "PIK3R3" 0.209664130751946 0.00419133300073679 -8.33763038160584 -1.21671727156375 -0.346216569376747 "NM_003629.3" ""
## "IGF1" 0.209664130751946 0.00469531002158976 -8.00485229097626 -1.35237657911683 -0.362554812155599 "NM_000618.3" ""
## "FGF9" 0.209664130751946 0.00537116735767449 7.62672834806593 -1.51431073362851 0.339856413911059 "NM_002010.2" ""
## "FOS" 0.209664130751946 0.00544472294336558 7.58942128541171 -1.53076055284833 0.717511561726223 "NM_005252.2" ""
## "LAMC3" 0.209664130751946 0.00558037220352611 7.52235208859716 -1.56055430020963 0.392993979437164 "NM_006059.3" ""
## "BMP8A" 0.209664130751946 0.00607566420976675 -7.29477701835583 -1.66381545159089 -0.514536983677777 "NM_181809.3" ""
## "SOCS1" 0.209664130751946 0.00639760207758428 -7.15970432874724 -1.72673693363771 -0.410208302721639 "NM_003745.1" ""
## "PLA1A" 0.209664130751946 0.00649110997675789 7.12215914175555 -1.74444918696743 1.19373379126119 "NM_015900.2" ""
## "MYB" 0.209664130751946 0.00669313623572217 -7.0434464274722 -1.78190248202152 -0.288096431832184 "NM_005375.2" ""
## "FGF21" 0.209664130751946 0.00683002871869916 -6.99188651363361 -1.80667362418531 -1.13437680738159 "NM_019113.2" ""
## "PLCG2" 0.209664130751946 0.00740900045639499 -6.78812313407085 -1.90645684402353 -0.638664102985267 "NM_002661.2" ""
## "WNT10B" 0.209664130751946 0.00760193562885115 -6.72487527440933 -1.93805729964667 -0.539806967105371 "NM_003394.2" ""
## "APH1B" 0.209664130751946 0.00774607553935676 -6.67900023645843 -1.96116838372613 -0.414092594795889 "NM_001145646.1" ""
## "SPP1" 0.209664130751946 0.0080620067964814 6.5823057715532 -2.01041466731431 0.316611528356276 "NM_000582.2" ""
## "NTRK2" 0.209664130751946 0.00808410007400517 -6.57573272675333 -2.01378886270794 -0.474078639365731 "NM_001007097.1" ""
## "TIAM1" 0.209664130751946 0.00826681682828336 6.52227167662832 -2.04135956959525 0.415780276730921 "NM_003253.2" ""
## "FGF13" 0.209664130751946 0.00828319933522009 -6.51755509760402 -2.043802905536 -0.236792730766778 "NM_033642.1" ""
## "ABL1" 0.209664130751946 0.00873578461255265 6.39195669762856 -2.10952769073832 0.241767119089825 "NM_005157.3" ""
## "NOTCH2" 0.209664130751946 0.00900007515786481 6.32254077783988 -2.14640779510234 0.438855594484702 "NM_024408.3" ""
## "THBS1" 0.209664130751946 0.00908521411734356 6.30075307871879 -2.15806632154826 0.241876365631319 "NM_003246.2" ""
## "HSPA2" 0.209664130751946 0.00928498490390841 6.25067754561821 -2.18501339475947 0.53484737445056 "NM_021979.3" ""
## "TGFB2" 0.209664130751946 0.00928568822374753 6.25050378008517 -2.18510727343565 0.40087217691341 "NM_003238.2" ""
## "CCND3" 0.209664130751946 0.00930948534952681 6.24463462301547 -2.18827965951766 0.254993425378244 "NM_001760.2" ""
## "E2F5" 0.209664130751946 0.00961575883880462 6.17083076796024 -2.22842419860223 0.281461214024381 "NM_001951.3" ""
## "JUN" 0.209664130751946 0.00993020295731684 6.09823377982331 -2.26837373784726 0.299459706476872 "NM_002228.3" ""
## "IFNG" 0.209664130751946 0.0104126987889864 -5.99257131306891 -2.32735346855391 -2.99986143518683 "NM_000619.2" ""
## "PPP2CB" 0.209664130751946 0.0104211457350577 5.9907795870004 -2.3283622469577 0.280177682472237 "NM_001009552.1" ""
## "PRL" 0.209664130751946 0.0107073996106906 -5.93117503383608 -2.3620875763561 -1.64664247821621 "NM_000948.3" ""
## "DKK4" 0.209664130751946 0.0109270643332908 -5.88684957976975 -2.38737943994024 -0.272240812981186 "NM_014420.2" ""
## "ETS2" 0.209664130751946 0.0112018938312688 5.83302682789381 -2.41833633904696 0.223715410422413 "NM_005239.4" ""
## "WNT10A" 0.209664130751946 0.012183025441512 -5.65427731974922 -2.52312653159868 -0.431009075748783 "NM_025216.2" ""
## "LAMA5" 0.209664130751946 0.0132079243602394 5.48682808940298 -2.62414594033513 0.349786014741899 "NM_005560.3" ""
## "CREB5" 0.209664130751946 0.013342089355477 -5.46618103900977 -2.63679905960324 -0.436996346240472 "NM_182898.2" ""
## "PITX2" 0.209664130751946 0.0133529396477425 -5.46452325220951 -2.63781690644146 -0.304682233994035 "NM_000325.5" ""
## "CHUK" 0.209664130751946 0.0133999672046415 5.45735856022952 -2.64221914617768 0.20263858040072 "NM_001278.3" ""
## "IRAK2" 0.209664130751946 0.0134776478532142 -5.44559630616313 -2.64945781615457 -0.255794422640509 "NM_001570.3" ""
## "LEFTY1" 0.209664130751946 0.0136576175905745 5.41868645107395 -2.66607263498487 1.49770467014306 "NM_020997.2" ""
## "DLL3" 0.209664130751946 0.0138045730707478 -5.39705806726938 -2.67948137775564 -0.579069526886043 "NM_203486.2" ""
## "TBL1XR1" 0.209664130751946 0.0140705999775044 5.35866818462127 -2.70340282330875 0.240775108221039 "NM_024665.4" ""
## "MAP3K5" 0.209664130751946 0.0140777651808985 5.35764746455451 -2.70404098039293 0.304861468551572 "NM_005923.3" ""
## "ITGA9" 0.209664130751946 0.0142032352196819 -5.33988402506303 -2.71516446545794 -0.288143217065699 "NM_002207.2" ""
## "FGF3" 0.209664130751946 0.0147036734121572 -5.27104248299813 -2.75859230181443 -0.201657972776001 "NM_005247.2" ""
## "MAP2K2" 0.209664130751946 0.0150104100712554 -5.2303569466169 -2.78449941360306 -0.223133210488076 "NM_030662.2" ""
## "CDC7" 0.209664130751946 0.0153625277011403 5.18498315990424 -2.81360592561083 0.203232000130827 "NM_003503.2" ""
## "JAK1" 0.209664130751946 0.0155033961966599 5.16721325827381 -2.82506707533966 0.20659919612155 "NM_002227.1" ""
## "RUNX1T1" 0.209664130751946 0.0155292049818096 -5.16398066927002 -2.8271557919878 -0.573199950950682 "NM_004349.2" ""
## "TSC1" 0.209664130751946 0.0155990553406174 -5.15526721583098 -2.83279173820481 -0.200044202514219 "NM_000368.3" ""
## "VHL" 0.209664130751946 0.0161822153689267 5.08447287558 -2.87889827239415 0.245452934229492 "NM_000551.2" ""
## "DKK2" 0.209664130751946 0.0163148988696443 -5.0688338428417 -2.88916009056349 -0.628051401685004 "NM_014421.2" ""
## "MET" 0.209664130751946 0.0163931862374308 5.05968470880096 -2.89517639323621 0.444075330671934 "NM_000245.2" ""
## "BMP4" 0.209664130751946 0.0167083759779296 5.0234237990194 -2.91911535726414 0.324963381631637 "NM_001202.2" ""
## "GHR" 0.209664130751946 0.0167417346151057 -5.01963881401942 -2.92162288444762 -0.522987907983277 "NM_000163.2" ""
## "SFN" 0.209664130751946 0.0168480105068528 5.00764629588771 -2.92957879468839 0.187670421319776 "NM_006142.3" ""
## "IL2RB" 0.21329856479031 0.0174552789021012 -4.94098014904721 -2.97411105719638 -0.730249943012394 "NM_000878.2" ""
## "OSM" 0.21329856479031 0.0176841922338905 4.91663732987981 -2.9905020091668 0.675130922574021 "NM_020530.3" ""
## "MAP2K1" 0.21744945847674 0.0184981747176826 -4.83332487630258 -3.04713449209709 -0.235855561411267 "NM_002755.2" ""
## "CACNA1E" 0.21744945847674 0.0196633905972771 4.72210213061536 -3.12405416667442 0.310721494405255 "NM_000721.2" ""
## "NTF3" 0.21744945847674 0.0196772329187974 -4.72083321717505 -3.12494054405341 -0.379380293602625 "NM_002527.4" ""
## "SRSF2" 0.21744945847674 0.019817787306712 4.70801473367268 -3.13390594819382 0.197435648863836 "NM_003016.3" ""
## "PGF" 0.21744945847674 0.0199149980206114 4.69921878745686 -3.14006983504426 0.587822136155656 "NM_002632.5" ""
## "RASGRP1" 0.21744945847674 0.0199929094135984 4.69220969844661 -3.1449885032613 0.301711593874854 "NM_005739.3" ""
## "COL1A1" 0.21744945847674 0.0202190819329231 4.67206413863159 -3.15916017693444 0.546057140544487 "NM_000088.3" ""
## "ATR" 0.21744945847674 0.0202472072306148 4.66957965309413 -3.16091146841827 0.179643620227848 "NM_001184.2" ""
## "HELLS" 0.217525797225053 0.0205317716768545 4.64469430457647 -3.17849605160511 0.397076925322438 "NM_018063.3" ""
## "SIRT4" 0.218767119492959 0.0209279769923111 -4.6107896553446 -3.20258074742269 -0.473531006858755 "NM_012240.1" ""
## "MAPK3" 0.221371717855219 0.0218411997590252 -4.53575061592563 -3.25641208524954 -0.221332083979123 "NM_001040056.1" ""
## "POS_A" 0.221371717855219 0.0219505169351756 4.52704397434326 -3.26270543310217 0.189140342088736 "" "ERCC_00117.1"
## "GDF6" 0.221371717855219 0.0222798867780555 -4.50115080954152 -3.28148034257684 -0.592244076075132 "NM_001001557.2" ""
## "POS_D" 0.221371717855219 0.0224758815270561 4.48597959747909 -3.29252189717887 0.210162363787665 "" "ERCC_00092.1"
## "POLR2J" 0.221371717855219 0.022588950801553 4.47730591883782 -3.29884825106338 0.281102350017772 "NM_006234.4" ""
## "SFRP1" 0.223176534253174 0.0230577796868713 -4.44193884790286 -3.32474760867241 -0.505037211109986 "NM_003012.3" ""
## "SOCS3" 0.223244008496892 0.0233937720477714 4.41716654167331 -3.34298800853026 0.989419205251536 "NM_003955.3" ""
## "FGF8" 0.223244008496892 0.0236342508995434 -4.39972042520006 -3.3558835335009 -0.943249137213076 "NM_033163.3" ""
## "IL12RB2" 0.230822477280229 0.0249210693620473 -4.31015636397035 -3.42273795779083 -0.933209146671777 "NM_001559.2" ""
## "BMP5" 0.230822477280229 0.0250253961336982 4.30316079481413 -3.42800613140478 0.549447307276783 "NM_021073.2" ""
## "PIK3R2" 0.232960477568158 0.0255543381005888 -4.26827010157306 -3.45438280235149 -0.190118959284007 "NM_005027.2" ""
## "CCNA1" 0.240040763599186 0.0270175381167741 -4.17646949466228 -3.52459828751231 -0.354841710793854 "NM_003914.3" ""
## "CDKN2B" 0.240040763599186 0.027054845113837 4.17421413624147 -3.52633838212887 0.177431660928812 "NM_004936.3" ""
## "TGFB1" 0.240040763599186 0.0277476896019409 -4.13305182954035 -3.5582247492014 -0.310609259519218 "NM_000660.3" ""
## "COL4A4" 0.240040763599186 0.0280808739253248 -4.11373125822283 -3.57327559186622 -0.4950971211902 "NM_000092.4" ""
## "PRDM1" 0.240040763599186 0.0280879337405053 4.11332511222105 -3.5735925619375 0.335328204060634 "NM_182907.1" ""
## "NASP" 0.240040763599186 0.02857951628717 4.08536746799718 -3.59546926099437 0.211947634571342 "NM_172164.1" ""
## "FGFR3" 0.240040763599186 0.0287675741023077 4.07483726145094 -3.60373862121226 0.163593947967241 "NM_022965.2" ""
## "GPC4" 0.240040763599186 0.0289722607227368 -4.06347734379081 -3.61267774396754 -0.269885352346654 "NM_001448.2" ""
## "IL1RAP" 0.240040763599186 0.0290865721197993 -4.05717854445561 -3.61764242588736 -0.227445683755557 "NM_002182.2" ""
## "PLA2G4A" 0.241352985956389 0.0301209230885996 4.0016102439869 -3.66169456376134 0.185657207336563 "NM_024420.2" ""
## "MDC1" 0.241352985956389 0.0303754894359431 3.98831399432868 -3.67230315902695 0.147850420264026 "NM_014641.2" ""
## "MEN1" 0.241352985956389 0.0305281101937883 -3.98041174977475 -3.67862056976554 -0.199436875917687 "NM_130802.2" ""
## "TMPRSS2" 0.241352985956389 0.0307253608599138 -3.9702744696397 -3.68673844336211 -0.39123967233141 "NM_005656.2" ""
## "ETV1" 0.241352985956389 0.0309991587193592 -3.95634258925934 -3.69792014603181 -0.16365345127444 "NM_004956.4" ""
## "FANCB" 0.241352985956389 0.0311463735959048 3.94891768228156 -3.70389127800254 0.212652684889202 "NM_152633.2" ""
## "KIT" 0.241352985956389 0.0319098372399871 3.91113013317787 -3.73440907816314 0.219379279680497 "NM_000222.1" ""
## "SYK" 0.241352985956389 0.032084017954161 -3.90267338585744 -3.741268510278 -0.17386900416162 "NM_003177.3" ""
## "ERBB2" 0.241352985956389 0.0325502573439119 -3.88032703754925 -3.75944649336129 -0.378890816212376 "NM_004448.2" ""
## "ARID1B" 0.241352985956389 0.0331110558111069 -3.85399273432555 -3.78096659025376 -0.203726110296966 "NM_020732.3" ""
## "POS_F" 0.241352985956389 0.0332880482453295 3.8458013210105 -3.787682242111 0.493245326138562 "" "ERCC_00034.1"
## "WHSC1" 0.241352985956389 0.0333663999869417 3.84219313337973 -3.7906436591838 0.148874298540052 "NM_007331.1" ""
## "POS_C" 0.241352985956389 0.0338852168898293 3.81857513374315 -3.81007776333164 0.145362438545584 "" "ERCC_00002.1"
## "GADD45B" 0.241352985956389 0.0345313408926316 3.78980902765753 -3.83386481355907 0.19993059397191 "NM_015675.2" ""
## "HIST1H3G" 0.241352985956389 0.0345519550204487 3.78890276930175 -3.83461630244746 0.139092513371914 "NM_003534.2" ""
## "RFC3" 0.241352985956389 0.0347408881931993 3.78062920838741 -3.84148284299026 0.208858508677713 "NM_002915.3" ""
## "RXRG" 0.241352985956389 0.0347654694443416 -3.77955705872983 -3.84237344286715 -0.556435960910893 "NM_006917.3" ""
## "ID1" 0.241352985956389 0.0349074926330606 3.77338166729458 -3.84750663840666 0.227381444843585 "NM_002165.2" ""
## "HDAC3" 0.241352985956389 0.0350946943865157 3.76529138671552 -3.85424058642806 0.14511977418031 "NM_003883.2" ""
## "SUV39H2" 0.242054420715085 0.0355054316099933 3.74773483290389 -3.86888910383245 0.193448606955611 "NM_024670.3" ""
## "UBB" 0.244149729279537 0.0365913603485429 -3.70255715462581 -3.90680699927346 -0.168274604730428 "NM_018955.2" ""
## "BNIP3" 0.244149729279537 0.0366722017035514 -3.69926344126438 -3.90958407188155 -0.142521068073934 "NM_004052.2" ""
## "DTX1" 0.244149729279537 0.0370465908069721 -3.68413127510223 -3.92236482659102 -0.788275835953515 "NM_004416.2" ""
## "MPL" 0.244149729279537 0.0370584410513582 -3.68365554064031 -3.9227672270357 -1.31625259895407 "NM_005373.2" ""
## "CCNA2" 0.244345095363325 0.0373997594943864 -3.67003696442163 -3.93430182304848 -0.141878639673349 "NM_001237.2" ""
## "COL4A5" 0.246319163879689 0.0382731768194 3.63590718068486 -3.9633393050803 0.196071198292918 "NM_033381.1" ""
## "CCNB1" 0.246319163879689 0.0383678325965806 -3.63226889008484 -3.96644578052601 -0.139471767487482 "NM_031966.2" ""
## "MTMR14" 0.246319163879689 0.0386444606596962 -3.62170222498511 -3.97547998704467 -0.135718637397513 "NM_022485.3" ""
## "RBX1" 0.250036410741664 0.0395465751683244 -3.58791044126167 -4.00449212287804 -0.140032784088332 "NM_014248.2" ""
## "COL5A1" 0.250076514821066 0.0398718933069302 -3.57596775582262 -4.01478986795294 -0.529677922646707 "NM_000093.3" ""
## "POLB" 0.25131037742871 0.040566058810441 -3.5508995559135 -4.03648081967222 -0.15282667509795 "NM_002690.1" ""
## "CACNA1D" 0.25131037742871 0.0407097167518446 -3.54578071977501 -4.04092264915683 -1.51331867055198 "NM_000720.2" ""
## "NODAL" 0.255366286861041 0.041692454997721 -3.51137707635702 -4.07088757736453 -0.543050088596672 "NM_018055.3" ""
## "SOS2" 0.25704611601616 0.0422945777628631 -3.49080997678892 -4.0888941245061 -0.138908829293946 "NM_006939.2" ""
## "LEP" 0.260520907480238 0.0431986198627946 3.4606277592278 -4.11544533330241 2.6791337298931 "NM_000230.2" ""
## "CDKN2C" 0.264398600165106 0.0446930246630611 -3.41247616135799 -4.15811763289728 -0.349885036132145 "NM_001262.2" ""
## "B2M" 0.264398600165106 0.0449139560620683 -3.40553313632492 -4.16430253045625 -0.207216851929335 "NM_004048.2" ""
## "FANCL" 0.264398600165106 0.0449616169478584 3.4040410910108 -4.16563270927327 0.223569253293366 "NM_001114636.1" ""
## "POS_B" 0.264398600165106 0.045190577069036 3.39690161363171 -4.17200281569842 0.125519348323571 "" "ERCC_00112.1"
## "GNG4" 0.270989209532448 0.0467236127601977 3.35026554381801 -4.21382401311788 0.28725845625341 "NM_004485.2" ""
## "AKT1" 0.270989209532448 0.0475248654733721 -3.32666517531577 -4.23512763313356 -0.125480628297085 "NM_005163.2" ""
## "ITGA2" 0.270989209532448 0.0476865826601098 3.32196375272319 -4.23938278597105 0.22713656284491 "NM_002203.2" ""
## "MSH6" 0.270989209532448 0.047921642452624 3.31516644715914 -4.24554150355089 0.133335436622227 "NM_000179.1" ""
## "MAP3K8" 0.270989209532448 0.0480452807716967 3.31160828268012 -4.24876851494522 0.273719793063231 "NM_005204.2" ""
## "GTF2H3" 0.27099910047087 0.0487343651632143 -3.29198993023031 -4.26659964984949 -0.133104129897955 "NM_001516.3" ""
## "BMP7" 0.27099910047087 0.0487383586306029 -3.29187727297851 -4.26670223316943 -0.17335662989084 "NM_001719.1" ""
## "HRAS" 0.272039510397191 0.0493819369416519 -3.2738746185965 -4.28312285391931 -0.136049601364624 "NM_005343.2" ""
## "GNAQ" 0.272039510397191 0.0496194515137734 3.26730641718066 -4.2891276192225 0.221938786273654 "NM_002072.2" ""
## "PPP2R1A" 0.27216509169044 0.0499895066370196 -3.25715274144212 -4.29842478843389 -0.119594799082467 "NM_014225.3" ""
## "IL23A" 0.272220902562825 0.0503469781525633 -3.24743525883985 -4.30733906762977 -0.234812877404071 "NM_016584.2" ""
## "DUSP6" 0.273128241544899 0.0516017218753406 3.21401248408629 -4.33812278954051 0.123572765867534 "NM_001946.2" ""
## "CAPN2" 0.273128241544899 0.0524394329792245 -3.19227117502527 -4.35825040422077 -0.153170047750853 "NM_001748.4" ""
## "IRS1" 0.273128241544899 0.0527120705986721 3.18529084547855 -4.36472989075262 0.141040598382578 "NM_005544.2" ""
## "CCNE1" 0.273128241544899 0.0528370933528116 3.18210529287174 -4.36768966802353 0.162067358643254 "NM_001238.1" ""
## "SHC1" 0.273128241544899 0.052910298901288 -3.18024449538091 -4.36941939124382 -0.175362124399184 "NM_183001.4" ""
## "CASP3" 0.273128241544899 0.0533572804896479 -3.1689536140489 -4.37992775009354 -0.119546856711214 "NM_032991.2" ""
## "NRAS" 0.273128241544899 0.0534885879416229 3.16565967250194 -4.38299754770894 0.21904296108678 "NM_002524.3" ""
## "CDKN1C" 0.273128241544899 0.0536735620113717 -3.16103693142071 -4.38730888303637 -0.289248728894513 "NM_000076.2" ""
## "DUSP5" 0.273128241544899 0.0537089411360923 3.16015507701142 -4.38813175150063 0.482035339410174 "NM_004419.3" ""
## "ITGB4" 0.273128241544899 0.0539985681625756 -3.152963635689 -4.39484718341213 -0.148980495101906 "NM_001005731.1" ""
## "MAPK9" 0.274330785281636 0.0547749862558254 3.13392542239452 -4.41266840945741 0.132386070997338 "NM_139068.2" ""
## "SMC1A" 0.274330785281636 0.0549361393995113 -3.1300169542243 -4.416334795596 -0.161790259529338 "NM_006306.2" ""
## "SF3A3" 0.274367682340185 0.0552934870022312 -3.12140204975882 -4.42442545509444 -0.120786077330628 "NM_006802.2" ""
## "BDNF" 0.277347849229743 0.0562478418718484 -3.09873803221368 -4.44577174307551 -0.16726262244082 "NM_170732.4" ""
## "TP53" 0.284485954526933 0.0580583580667211 3.05705794142634 -4.48526134063087 0.131347486242959 "NM_000546.2" ""
## "RNF43" 0.286256314124107 0.0591595112357102 3.03250821625673 -4.50866229196508 0.112343533398668 "NM_017763.4" ""
## "MLLT4" 0.286256314124107 0.0595361284984459 3.02424462427654 -4.51656281670156 0.131756275860422 "NM_005936.2" ""
## "DLL1" 0.286256314124107 0.0597833621175861 -3.01885593305059 -4.52172116284141 -0.145525239715317 "NM_005618.3" ""
## "STAT4" 0.286256314124107 0.0598801473422876 -3.01675410956239 -4.52373451404138 -0.377925773188469 "NM_003151.2" ""
## "EPHA2" 0.289230735399832 0.0608712644655259 2.99547583562862 -4.54416049711333 0.238753555451014 "NM_004431.2" ""
## "MMP9" 0.295994735285708 0.0626723546650862 -2.95791088039739 -4.58041365208223 -2.12677055995356 "NM_004994.2" ""
## "CACNA2D3" 0.296842032264739 0.0632303818727186 2.94654898622947 -4.59142729986615 0.177397020681711 "NM_018398.2" ""
## "ARNT2" 0.304817079282919 0.0653179455606255 -2.90514404793885 -4.63175389229615 -0.164298379861402 "NM_014862.3" ""
## "MYC" 0.305810680404897 0.0659209247301372 2.8934951514841 -4.64315335068818 0.151971306859576 "NM_002467.3" ""
## "HES1" 0.31074984089349 0.0673819808059863 -2.86581896828789 -4.67033185446393 -0.155085331069367 "NM_005524.2" ""
## "RPS6KA5" 0.31830859759031 0.0696560780562699 -2.82421528997527 -4.71143861826612 -0.202771844620491 "NM_004755.2" ""
## "KDM6A" 0.31830859759031 0.0701609816568837 -2.81521029188279 -4.72037572956439 -1.80130107623833 "NM_021140.2" ""
## "KAT2B" 0.31830859759031 0.0702390145192904 -2.81382585407998 -4.72175098105122 -0.145268864944422 "NM_003884.3" ""
## "FANCA" 0.318463142115857 0.0706793198063254 2.80605021899628 -4.72948121207697 0.167478512728502 "NM_000135.2" ""
## "MYD88" 0.319092321806306 0.0712259646889076 -2.79648111304517 -4.73900886002545 -0.122112149780094 "NM_002468.3" ""
## "IL1R2" 0.322330762869423 0.0731667397702457 2.76323973124286 -4.77222967497051 0.310654763776713 "NM_173343.1" ""
## "FZD9" 0.322330762869423 0.0731835703135113 -2.76295632445815 -4.77251372951918 -0.320041786481363 "NM_003508.2" ""
## "CREB3L1" 0.322330762869423 0.0732952086214968 -2.76107853664061 -4.77439616042918 -0.189816449230393 "NM_052854.1" ""
## "PIK3CD" 0.322330762869423 0.0735933757061566 2.75608085208652 -4.77940917495184 0.407975648842557 "NM_005026.3" ""
## "ITGB8" 0.327357935749995 0.07529695444871 2.7280062540623 -4.80765010235999 0.23205209885954 "NM_002214.2" ""
## "CAMK2B" 0.327357935749995 0.0755762581259555 -2.72347947806545 -4.81221642732859 -0.258839513606121 "NM_001220.3" ""
## "CDKN2A" 0.33059921286513 0.076746245843691 2.70474260978524 -4.83115450631978 0.140584657822322 "NM_000077.3" ""
## "RELA" 0.331440355552358 0.0773642666659203 -2.69498921090113 -4.84103652046387 -0.192944264460563 "NM_021975.2" ""
## "SMO" 0.333541641096025 0.0786907551565172 -2.67438072319334 -4.86197039094997 -0.241710460473184 "NM_005631.3" ""
## "MPO" 0.333541641096025 0.078705616840261 -2.674152299132 -4.86220282876012 -1.94926904769438 "NM_000250.1" ""
## "IL20RB" 0.337353074239962 0.0800352956742767 2.65393083939335 -4.88281490222753 0.215095397251281 "NM_144717.2" ""
## "SOX9" 0.33830679173022 0.0806930740478969 2.64408219657434 -4.89287901577781 0.106030771565603 "NM_000346.2" ""
## "FUT8" 0.340806305543689 0.0821349896463365 -2.62283969261823 -4.91464233174184 -0.122667129086224 "NM_004480.4" ""
## "MMP7" 0.340806305543689 0.0824593620351191 -2.61812511186202 -4.91948286341075 -1.568514033951 "NM_002423.3" ""
## "PRKACA" 0.340806305543689 0.0825933648639042 -2.61618420387401 -4.92147671454582 -0.107546037881546 "NM_002730.3" ""
## "RAD51" 0.347740963511887 0.0849111943604936 2.58322147019335 -4.9554354888716 0.0941824322924081 "NM_133487.2" ""
## "WNT16" 0.347740963511887 0.0854167787574484 -2.57618021502196 -4.96271315044533 -0.254731490468133 "NM_057168.1" ""
## "TSPAN7" 0.347740963511887 0.0856045994359619 -2.5735776552345 -4.96540518823027 -0.684893718904391 "NM_004615.3" ""
## "MAP2K4" 0.352867939722101 0.0880904308817731 -2.53978783201556 -5.00045911644893 -0.185279638813666 "NM_003010.2" ""
## "CYLD" 0.352867939722101 0.0883121540413146 -2.53683165635035 -5.00353489383485 -0.118342101161021 "NM_015247.1" ""
## "RAD21" 0.352867939722101 0.0890435568932155 -2.52714506203797 -5.01362349767447 -0.169530575909187 "NM_006265.2" ""
## "WNT2B" 0.352867939722101 0.0895325423386578 -2.52072396349685 -5.02031960007028 -0.583465952716907 "NM_024494.1" ""
## "DDIT4" 0.352867939722101 0.0902977609803138 -2.51076239898492 -5.0307212000696 -0.368195397951322 "NM_019058.2" ""
## "FGF19" 0.352867939722101 0.0903483253393135 2.51010784822519 -5.03140523394122 0.169627079454346 "NM_005117.2" ""
## "BRCA2" 0.352867939722101 0.0905134471137302 2.50797352433871 -5.03363618180386 0.14728502211519 "NM_000059.3" ""
## "XPA" 0.352867939722101 0.0908954867677315 2.50305383551005 -5.03878142902298 0.133952718030036 "NM_000380.3" ""
## "HDAC5" 0.352867939722101 0.090917504877378 -2.5027710808343 -5.03907726760482 -0.266213312196861 "NM_005474.4" ""
## "H2AFX" 0.357470558878961 0.0925593411383024 2.48192277903302 -5.06092614619777 0.0899365975049307 "NM_002105.2" ""
## "TNFRSF10B" 0.358423948437777 0.0932880094070909 2.47281631261387 -5.07049178076265 0.188905284007495 "NM_003842.3" ""
## "NR4A1" 0.358423948437777 0.0937205477420208 -2.46745225764901 -5.07613256777766 -0.178085289832791 "NM_173157.1" ""
## "BAMBI" 0.360695383676607 0.0955352270591373 2.4452770686013 -5.09950081033298 0.0931585953964316 "NM_012342.2" ""
## "AXIN2" 0.360695383676607 0.0969711687102877 2.42809583051717 -5.11766035692922 0.113266207807033 "NM_004655.3" ""
## "FZD8" 0.360695383676607 0.0970012895008564 2.42773880168823 -5.11803821157858 0.156466517592866 "NM_031866.1" ""
## "COL4A6" 0.360695383676607 0.0972846863846191 2.42438631942655 -5.12158722984831 0.308481034823918 "NM_001847.2" ""
## "PHF6" 0.360695383676607 0.0974077311798849 2.42293449550621 -5.12312471619633 0.119398111972378 "NM_032335.3" ""
## "MLF1" 0.360695383676607 0.0974706238573144 -2.42219328934787 -5.12390978418986 -0.109659689708689 "NM_022443.3" ""
## "ACVR1C" 0.360695383676607 0.0975436390331576 -2.42133352706611 -5.12482053253444 -0.142305489327188 "NM_145259.2" ""
## "FN1" 0.360695383676607 0.0979950468407107 2.41603572097317 -5.13043508068705 0.0920451183704838 "NM_212482.1" ""
## "PIM1" 0.362154068594926 0.0992215411007209 -2.4017920516235 -5.14555218532069 -0.165599378109736 "NM_002648.2" ""
## "WT1" 0.362154068594926 0.0993152101376392 -2.40071317385923 -5.14669851360351 -0.156506865939487 "NM_000378.3" ""
## "POLD4" 0.362334740654369 0.100330816185932 -2.38909534977009 -5.15905415425232 -0.401764100723732 "NM_021173.2" ""
## "CACNB2" 0.362334740654369 0.100832147870488 -2.38341373884828 -5.16510421288854 -1.61165528269757 "NM_000724.3" ""
## "MCM2" 0.362334740654369 0.101115746294746 2.3802150872257 -5.1685124893262 0.0954545314093185 "NM_004526.2" ""
## "SHC3" 0.362334740654369 0.10136420337313 -2.37742184974144 -5.1714900731127 -0.152705216596225 "NM_016848.5" ""
## "MTOR" 0.362334740654369 0.102289809660268 2.36708955072755 -5.18251470023482 0.0975772695972967 "NM_004958.2" ""
## "AKT3" 0.362334740654369 0.103714844302876 2.35140497630854 -5.19928142429873 0.0922607150468622 "NM_181690.1" ""
## "MAP2K6" 0.362334740654369 0.103977218854889 -2.34854602920002 -5.20234165097273 -0.195208405112414 "NM_002758.3" ""
## "E2F1" 0.362334740654369 0.104468323718339 2.34321847580099 -5.20804757929905 0.177459398688606 "NM_005225.1" ""
## "STAT3" 0.362334740654369 0.104550595299181 2.34232899327658 -5.20900065212986 0.193035552785449 "NM_139276.2" ""
## "CACNB3" 0.362334740654369 0.104630409140591 2.34146690354955 -5.20992448757339 0.142680915829646 "NM_000725.2" ""
## "WIF1" 0.362334740654369 0.104660471251783 2.34114240428355 -5.21027225754451 0.336826638818287 "NM_007191.2" ""
## "DNMT1" 0.362334740654369 0.104966405792414 2.33784655021882 -5.21380536370483 0.0957697419436148 "NM_001379.2" ""
## "PRKAR1B" 0.362334740654369 0.105372858251526 -2.33348600110759 -5.21848231418823 -0.213914495971274 "NM_001164759.1" ""
## "IFNA2" 0.365827498942716 0.107090469812205 -2.31528412739305 -5.23803557781665 -0.430949174828379 "NM_000605.3" ""
## "PTEN" 0.365827498942716 0.107397395501604 -2.31206926173561 -5.24149423997911 -0.106192405247405 "NM_000314.3" ""
## "MNAT1" 0.365827498942716 0.107788459509907 2.3079893663437 -5.24588572633489 0.0892107890679181 "NM_002431.2" ""
## "CDC6" 0.372231365705903 0.110150098015012 2.28373002432376 -5.27204813796363 0.100869896236816 "NM_001254.3" ""
## "FANCE" 0.378842471292657 0.112718631492128 -2.25805705280418 -5.29982761802579 -0.221683384892081 "NM_021922.2" ""
## "GNAS" 0.378842471292657 0.113333220049126 -2.25201991378369 -5.3063737254538 -0.102870437018584 "NM_080425.1" ""
## "STMN1" 0.378842471292657 0.113556097900222 -2.24984043200687 -5.30873821210958 -0.0841109329270449 "NM_203401.1" ""
## "CDC25C" 0.383793082968143 0.115529550485308 -2.23076707660329 -5.32945891784101 -0.119683232203192 "NM_001790.2" ""
## "HES5" 0.385494236626601 0.116769040479024 -2.21898919639536 -5.34227916559354 -0.160872066392413 "NM_001010926.3" ""
## "WHSC1L1" 0.385494236626601 0.11725939358735 2.21437169041159 -5.34731050581646 0.0870216689753729 "NM_017778.2" ""
## "DDB2" 0.385494236626601 0.117819893162934 -2.20912231445591 -5.35303386140753 -0.145911916555502 "NM_000107.1" ""
## "EPO" 0.385494236626601 0.118113576613487 2.2063839203189 -5.35602099047704 1.77489742649003 "NM_000799.2" ""
## "PLCB1" 0.385494236626601 0.118801940742975 2.19999770338448 -5.36299120171835 0.280403054646552 "NM_182734.1" ""
## "CEBPA" 0.385494236626601 0.119070208954034 -2.1975210400146 -5.36569581641512 -0.277474206648345 "NM_004364.2" ""
## "RPS27A" 0.385494236626601 0.119732081671673 -2.19143947835243 -5.37234059093559 -0.0845823206559295 "NM_002954.5" ""
## "FGF2" 0.385494236626601 0.119975247113381 2.18921541770246 -5.37477184765469 0.10575927914477 "NM_002006.4" ""
## "ETV7" 0.38676670047711 0.121198334452897 2.17811106455469 -5.38692044899202 0.156127414696555 "NM_016135.2" ""
## "FGF7" 0.38676670047711 0.1217463711017 -2.17317947116773 -5.39232098348163 -2.68700506611572 "NM_002009.3" ""
## "HNF1A" 0.38676670047711 0.121865612479255 -2.172110023331 -5.39349254157769 -1.7009556314488 "NM_000545.4" ""
## "RAD50" 0.38676670047711 0.12234456851827 2.16782712164283 -5.39818585706378 0.127825342753498 "NM_005732.2" ""
## "POLR2H" 0.388810560148377 0.123487027394063 2.15769256153004 -5.40930097941575 0.0946621929260232 "NM_001278698.1" ""
## "MAML2" 0.390827321140849 0.124626059037261 -2.14770077562034 -5.42027233357469 -0.0820968901619139 "NM_032427.1" ""
# Visualize and quality control test results.
# Build histogram of P-values for all genes. Normal test
# assumption is that most genes are not differentially expressed.
tT2 <- topTable(fit2, adjust="fdr", sort.by="B", number=Inf)
hist(tT2$adj.P.Val, col = "grey", border = "white", xlab = "P-adj",
ylab = "Number of genes", main = "P-adj value distribution")
# summarize test results as "up", "down" or "not expressed"
dT <- decideTests(fit2, adjust.method="fdr", p.value=0.05, lfc=0)
# Venn diagram of results
vennDiagram(dT, circle.col=palette())
# create Q-Q plot for t-statistic
t.good <- which(!is.na(fit2$F)) # filter out bad probes
qqt(fit2$t[t.good], fit2$df.total[t.good], main="Moderated t statistic")
# volcano plot (log P-value vs log fold change) ###mUESTRA A LA IZQUIERDA LOS GENES DOWN REGULATION Y A LA DERECHA LOS UP REGULATION
colnames(fit2) # list contrast names
## [1] "tto1-tto2"
ct <- 1 # choose contrast of interest
volcanoplot(fit2, coef=ct, main=colnames(fit2)[ct], pch=20,
highlight=length(which(dT[,ct]!=0)), names=rep('+', nrow(fit2)))
