[BioC] Limma: topTable without eBayes?

[Gordon K Smyth]

Why would you need or want to do that?  eBayes doesn't destroy any 
information, so why do you need to avoid it?

Gordon

> Date: Tue, 31 Aug 2010 19:51:55 +0200
> From: "Hooiveld, Guido" <Guido.Hooiveld at wur.nl>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Limma: topTable without eBayes?
> Content-Type: text/plain
>
> 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 at wur.nl

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