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Guido Hooiveld
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4.1k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
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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