Job tag is for job offers. Please, change it to question :).

I think you should give details of your data and design. Otherwise it will impossible for us to help you

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IQRs <- esApply(data.gcrma,1,IQR)

f3 <- function(x)( IQR(x) > median(IQRs) )
selected3 <- genefilter(data.gcrma, f3)
sum(selected3)

gcrmaf3 <- (data.gcrma[selected3,])
dim(data.gcrma)

Features  Samples
   54675       56 

dim(gcrmaf3)

Features  Samples
   27337       56

library(limma)

arrayw <- arrayWeights(data.gcrma)
targets <- readTargets("phenoDataRTC.txt")
sibShip <- factor(targets$sibShip)
Disease <- factor(targets$Disease, levels=c("N","L"))
design <- model.matrix(~sibShip+Disease)
design

(Intercept) sibShip7 sibShip8 sibShip10 sibShip11 sibShip12 sibShip13 sibShip15
1            1        0        0         0         0         0         0         0
2            1        0        0         0         0         0         0         0
3            1        1        0         0         0         0         0         0
4            1        1        0         0         0         0         0         0
5            1        0        1         0         0         0         0         0
6            1        0        1         0         0         0         0         0
7            1        0        0         1         0         0         0         0
8            1        0        0         1         0         0         0         0
9            1        0        0         0         1         0         0         0
10           1        0        0         0         1         0         0         0
11           1        0        0         0         0         1         0         0
12           1        0        0         0         0         1         0         0
13           1        0        0         0         0         0         1         0
14           1        0        0         0         0         0         1         0
15           1        0        0         0         0         0         0         1
16           1        0        0         0         0         0         0         1
17           1        0        0         0         0         0         0         0
18           1        0        0         0         0         0         0         0
19           1        0        0         0         0         0         0         0
20           1        0        0         0         0         0         0         0
21           1        0        0         0         0         0         0         0
22           1        0        0         0         0         0         0         0
23           1        0        0         0         0         0         0         0
24           1        0        0         0         0         0         0         0
25           1        0        0         0         0         0         0         0
26           1        0        0         0         0         0         0         0
27           1        0        0         0         0         0         0         0
28           1        0        0         0         0         0         0         0

   sibShip17 sibShip19 sibShip20 sibShip21 sibShip22 sibShip23 DiseaseL
1          0         0         0         0         0         0        0
2          0         0         0         0         0         0        1
3          0         0         0         0         0         0        0
4          0         0         0         0         0         0        1
5          0         0         0         0         0         0        0
6          0         0         0         0         0         0        1
7          0         0         0         0         0         0        0
8          0         0         0         0         0         0        1
9          0         0         0         0         0         0        0
10         0         0         0         0         0         0        1
11         0         0         0         0         0         0        0
12         0         0         0         0         0         0        1
13         0         0         0         0         0         0        0
14         0         0         0         0         0         0        1
15         0         0         0         0         0         0        0
16         0         0         0         0         0         0        1
17         1         0         0         0         0         0        0
18         1         0         0         0         0         0        1
19         0         1         0         0         0         0        0
20         0         1         0         0         0         0        1
21         0         0         1         0         0         0        0
22         0         0         1         0         0         0        1
23         0         0         0         1         0         0        0
24         0         0         0         1         0         0        1
25         0         0         0         0         1         0        0
26         0         0         0         0         1         0        1
27         0         0         0         0         0         1        0
28         0         0         0         0         0         1        1

attr(,"assign")
 [1] 0 1 1 1 1 1 1 1 1 1 1 1 1 1 2

attr(,"contrasts")

attr(,"contrasts")$sibShip
[1] "contr.treatment"

attr(,"contrasts")$Disease
[1] "contr.treatment"

fit <- lmFit(gcrmaf3, design,  weights=arrayw)
fits <-eBayes(fit)