Dear all, i have problem in comparing two toptable toptable A data<-ReadAffy(widget=T) data.rma<-rma(data) design <- cbind(WT=c(0,0,1,1),MU=c(1,1,0,0)) colnames(design) <- c("WT","MU") fit <- lmFit(data.rma, design) cont.matrix <- makeContrasts(MUvsWT=MU-WT, levels=design) cont.matrix fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) topTable(fit2, adjust="BH") topTable(fit2, adjust="BH",confint=TRUE) ID logFC CI.025 CI.975 AveExpr t P.Value 9878 1377329_at 6.471733 6.285806 6.657660 7.237431 68.22231 5.128839e-10 7779 1375230_at 6.021966 5.799411 6.244521 7.699632 53.03330 2.372552e-09 5602 1373053_at 3.943716 3.772685 4.114748 9.863075 45.19368 6.271905e-09 18553 1386128_at -3.451197 -3.627397 -3.274997 6.755917 -38.38945 1.689248e-08 10322 1377774_at 4.027673 3.812603 4.242744 9.383797 36.70470 2.217963e-08 28230 1396344_at -3.598380 -3.793991 -3.402770 5.265303 -36.05482 2.471829e-08 16850 1384309_at -3.665845 -3.877730 -3.453960 6.425085 -33.90959 3.585708e-08 23580 1391512_at -3.120271 -3.302527 -2.938015 5.871875 -33.55511 3.821572e-08 3686 1371137_at 3.838997 3.609084 4.068909 6.590163 32.72682 4.446685e-08 1751 1369202_at 3.881571 3.631429 4.131713 6.100156 30.41373 6.932570e-08 adj.P.Val B 9878 1.595018e-05 10.405175 7779 3.689199e-05 10.000273 5602 6.501666e-05 9.653808 18553 1.281190e-04 9.217486 10322 1.281190e-04 9.081870 28230 1.281190e-04 9.025965 16850 1.485588e-04 8.825615 23580 1.485588e-04 8.789987 3686 1.536527e-04 8.703707 1751 2.044349e-04 8.438207 ### NOW I TAKE THE LIST CONTAINING ONLY THE GENES THAT I WOULD LIKE TO COMPARE IN THE NEXT ANALISYS ### geni<-topTable(fit2, adjust="BH",confint=TRUE)$ID > geni [1] "1377329_at" "1375230_at" "1373053_at" "1386128_at" "1377774_at" [6] "1396344_at" "1384309_at" "1391512_at" "1371137_at" "1369202_at" ### i load the next dataset ### data1<-ReadAffy(widget=T) data1.rma<-rma(data1) fit1 <- lmFit(data1.rma, design) fit12 <- contrasts.fit(fit1, cont.matrix) fit12 <- eBayes(fit12) topTable(fit12, adjust="BH") fit12 ### i select in the second toptable only the genes that i have found in the first toptable ### fit12[geni,] topTable(fit12[geni,], adjust="BH") toptable B ID logFC CI.025 CI.975 AveExpr t 5 1377774_at 0.59097177 0.42056801 0.76137553 7.420289 6.7972876 9 1371137_at 0.35342217 0.18354810 0.52329624 3.910452 4.0776955 3 1373053_at 0.14288085 -0.03031712 0.31607882 7.923810 1.6168857 10 1369202_at 0.29962748 -0.11431021 0.71356517 3.526088 1.4187137 1 1377329_at 0.23248032 -0.09254813 0.55750878 3.740884 1.4018867 8 1391512_at -0.09952800 -0.27547764 0.07642164 7.373388 -1.1086769 7 1384309_at 0.08555764 -0.08479778 0.25591306 8.014597 0.9843532 4 1386128_at -0.09997307 -0.30833095 0.10838482 8.220204 -0.9404185 6 1396344_at -0.09588201 -0.30467205 0.11290802 6.850412 -0.9000683 2 1375230_at -0.05188944 -0.22442774 0.12064887 3.864847 -0.5894426 P.Value adj.P.Val B 5 0.0006301981 0.006301981 -3.000510 9 0.0073493692 0.036746846 -3.402337 3 0.1599104563 0.426525478 -4.370428 10 0.2085487414 0.426525478 -4.473515 1 0.2132627388 0.426525478 -4.482193 8 0.3123780439 0.449663059 -4.628625 7 0.3650716821 0.449663059 -4.686366 4 0.3853275454 0.449663059 -4.705891 6 0.4046967527 0.449663059 -4.723360 2 0.5782805807 0.578280581 -4.839556 now i have two toptable with the same genes i would like to know if there is a way in order to create a table with 5 columns: 1° column: geneName 2° column: logFC (for the first analisys) 3° column: logFC (for the second analisys) for the first 3 columns there are no problems, but now i would like to obtain: 4° column: Here a value estimate the% change in each gene (comparing the logFC from Column 3 respect to the logFC from Column 2) 5° column: only if it is possible, to have a statistical value that can compare column 3 with respect to 2 thanks a lot for the help! > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools tcltk stats graphics grDevices utils datasets [8] methods base other attached packages: [1] rat2302cdf_2.9.1 AnnotationDbi_1.16.8 tkWidgets_1.32.0 [4] DynDoc_1.32.0 widgetTools_1.32.0 multtest_2.10.0 [7] factDesign_1.30.0 affyPLM_1.30.0 preprocessCore_1.16.0 [10] gcrma_2.26.0 vsn_3.22.0 affy_1.32.0 [13] limma_3.10.0 RColorBrewer_1.0-5 GeneMeta_1.26.0 [16] genefilter_1.36.0 Biobase_2.14.0 BiocInstaller_1.2.1 [19] metafor_1.6-0 Formula_1.0-1 nlme_3.1-102 loaded via a namespace (and not attached): [1] affyio_1.22.0 annotate_1.32.0 Biostrings_2.22.0 DBI_0.2-5 [5] grid_2.14.0 IRanges_1.12.4 lattice_0.20-0 MASS_7.3-16 [9] RSQLite_0.11.0 splines_2.14.0 survival_2.36-10 xtable_1.6-0 [13] zlibbioc_1.0.0 -- ----------------------------------------------------- Dr. Alberto Goldoni Parma, Italy ----------------------------------------------------- [[alternative HTML version deleted]]