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




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