Hi, I have got question about several comparisons and results : I have got 4 groups and I want to make several comparisons between my groups (gp1 vs gp2, gp1 vs gp3, ...). I tested decideTest in order to have easy resume output but I don't understand why in a decideTest I obtain results not coording topTable output. fit <- lmFit(data_i,mat_group) comparaison <- makeContrasts(N-Ta,N-T1,N-T2,Ta-T1,Ta-T2,T1-T2,levels=mat_group) fit2 <- contrasts.fit(fit,comparaison) fit2 <- eBayes(fit2) top_table <- topTable(fit2,coef=1,number=Inf,adjust="BH") rownames(top_table)<- top_table[,1] ID logFC AveExpr t P.Value adj.P.Val B IGF1R 0.111104650376149 6.73735754086491 0.58031824032662 0.563347919004554 0.89178337590619 -5.80922017018552 IGF2R -0.418361001891785 7.30781700757716 -1.89591269242418 0.0616198608368053 0.566570014038297 -4.30516165436281 INSR -0.104189972020608 5.88324657993507 -0.705621827997018 0.482494171926321 0.858963516232972 -5.73329527131923 IGF1 0.0164024330700565 5.32379121221856 0.0580159806673495 0.953882062264167 0.993280048337664 -5.96683923009462 IGF2 -2.03692409239562 7.64672458332555 -2.78687079989285 0.00665914505810975 0.255548599553939 -2.46861977043762 INS 1.65128828436572 6.65133927223272 2.04732749311482 0.0439423770026206 0.508760608526091 -4.03635411033303 IGFBP1 0.111163236117028 3.7608601464086 0.990350899711699 0.325019419965225 0.79173927409954 -5.50673419683211 IGFBP2 1.4347995251779 7.54793353816003 3.06683251663792 0.00295982828163497 0.16458256036792 -1.77287225505653 IGFBP3 -0.875527979281101 10.4136969590099 -1.72885747148627 0.0877319854057766 0.615890064783784 -4.57990448008225 IGFBP4 -1.06382888423619 10.6781825579171 -3.59228487330552 0.000567234252702273 0.0858624589183034 -0.332444870299646 IGFBP5 0.0461190965231344 6.75488133496068 0.100191694176698 0.920445389165695 0.988013212218042 -5.96367782236715 IGFBP6 -0.333902382597201 7.18472204506767 -0.793175371995814 0.430046033425277 0.842849113060914 -5.67158345971083 IGFBP7 -2.06010861248481 9.26037314643127 -6.8481256400995 1.44348094893832e-09 2.94975331915545e-06 11.1853303363173 IGF2BP3 -0.0148502449143448 4.54849676079719 -0.031861021350583 0.974663058942624 0.997732729342142 -5.96795306155805 results <- decideTests(fit2,method="nestedF",adjust="BH",p.value=0.05,lfc=0) results[intersect(liste_genes_interest,rownames(results)),] N - Ta N - T1 N - T2 Ta - T1 Ta - T2 T1 - T2 IGF1R 0 0 1 1 1 0 IGF2R 0 -1 0 0 0 1 INSR 0 0 0 0 0 0 IGF1 0 0 0 0 0 0 IGF2 -1 0 0 0 1 0 INS 0 0 0 0 0 0 IGFBP1 0 0 0 0 0 0 IGFBP2 1 1 1 0 1 1 IGFBP3 0 0 0 0 0 0 IGFBP4 -1 0 0 1 1 0 IGFBP5 0 0 0 0 0 0 IGFBP6 0 0 0 0 0 0 IGFBP7 -1 -1 -1 -1 -1 0 IGF2BP3 0 0 0 0 -1 -1 -- -- Elodie Chapeaublanc IE Bioinformatique Équipe Oncologie Moléculaire Institut Curie - UMR 144 - CNRS 26 rue d'Ulm - 75248 Paris Cedex 05 Tel: +33 1 56 24 63 57 Email: elodie.chapeaublanc@curie.fr [[alternative HTML version deleted]]