Dear list,

topTable is a convenient function for displaying the top regulated genes in an experiment. topTable is usually applied on a object that is generated after fitting a linear model AND subsequent application of the eBayes funtion (fit3 below).
I would like to view the results of a model WITHOUT applying the eBayes function, preferably using topTable. That is, using topTable to summerize the results of fit2 below. Applying topTable as such won't work; apparently a format imposed by the eBayes function is required to have topTable properly work. Even specifying a contrast of interest doesn't work.
Therefore, has anyone a suggestion how to summerize the results of the fit2 mentioned below?

Thanks,
Guido

> library(affy)
> library(limma)
> targets <- readTargets("targets_A23.txt")
>
> affy.data <- ReadAffy(filenames=targets$FileName)
> x.norm <- rma(affy.data)
Background correcting
Normalizing
Calculating Expression
>
> TS <- paste(targets$Strain, targets$Treatment, sep=".")
> TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY"))
> design <- model.matrix(~0+TS)
> colnames(design) <- levels(TS)
> fit <- lmFit(x.norm, design)
> cont.matrix <- makeContrasts(A=WT.WY-WT.Con, B=KO.WY-KO.Con, levels=design)
>
> fit2 <- contrasts.fit(fit, cont.matrix)  #<<---- how to conviently summerize results of this fit?
>
> fit3 <- eBayes(fit2)
>
> topTable(fit3)
                ID        A            B  AveExpr         F      P.Value    adj.P.Val
13289 1431833_a_at 3.538370 -0.091190845 7.856618 1453.7786 5.084771e-18 1.153734e-13
18706 1450643_s_at 2.847376  0.182291682 7.907519 1234.5101 1.739465e-17 1.620566e-13
17177   1449065_at 4.528581  0.125074564 6.713129 1200.7506 2.142661e-17 1.620566e-13
7120  1422925_s_at 3.149781 -0.007867198 8.072523  895.1004 1.945926e-16 1.103827e-12
7192  1422997_s_at 4.298410  0.090012125 8.311977  837.9040 3.193016e-16 1.448991e-12
13047 1431012_a_at 2.682180  0.228653000 8.911287  785.9448 5.159295e-16 1.698832e-12
6721    1422526_at 2.772829  0.123117132 8.060643  784.2985 5.240997e-16 1.698832e-12
16494   1448382_at 3.386068  0.193350865 9.658716  685.0981 1.442685e-15 3.703026e-12
296     1415965_at 3.749143  0.071163645 5.293939  683.4572 1.468807e-15 3.703026e-12
8911    1424716_at 2.647513  0.370083995 8.453969  665.2223 1.798165e-15 4.080035e-12
> topTable(fit2)
Error in topTableF(fit, number = number, genelist = genelist, adjust.method = adjust.method,  :
  F-statistics not available. Try topTable for individual coef instead.
> topTable(fit2, coef=1)
Error in dim(data) <- dim : attempt to set an attribute on NULL
>
> sessionInfo()
R version 2.11.0 (2010-04-22)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] moe430acdf_2.6.0 limma_3.4.0      affy_1.26.1      Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.11.0
>


------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
internet:   http://nutrigene.4t.com<http://nutrigene.4t.com/>
email:      guido.hooiveld@wur.nl



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