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Last seen 9.7 years ago
Hello,
Please could you explain me why the no. of Differentially expressed
genes in my data varying when in one i at one step
i am using "arrayWeight" function,
and for the same data without using "arrayWeight"fucntion.
Which one is more reliable???
Here is my code::
###################
> DiffEx_all <- data.matrix(read.csv("Log2AvgSig
afterNorm.csv",row.names=1))
> DiffEx_allgp <- substr(colnames(DiffEx_all),1,5)
> DiffEx_allgp <- as.factor(DiffEx_allgp)
> DiffEx_allgp
[1] D1_R. D2_NR D2_R D2_NR D2_NR D1_NR D1_R. D1_NR D1_NR Contr Contr
Contr
Levels: Contr D1_NR D1_R. D2_NR D2_R
> DiffEx.design <- model.matrix(~0+DiffEx_allgp)
>
colnames(DiffEx.design)=sub("DiffEx_allgp","",colnames(DiffEx.design))
> DiffEx.design
#####################################
DE analysis with "arrayWeights"
#####################################
> aw=arrayWeights(DiffEx_all,DiffEx.design)
> fit.all <-lmFit(DiffEx_all,DiffEx.design,weights=aw)
> ebfit.all <- eBayes(fit.all)
> all_contrasts <- makeContrasts(D1R= D1_R.-Contr,D1NR=D1_NR-Contr,D2R
=D2_R-Contr,D2NR=D2_NR-Contr,levels=DiffEx.design)
> ebfit.all.contrasts <- contrasts.fit(ebfit.all, all_contrasts)
> ebfit.all.contrasts <- eBayes(ebfit.all.contrasts)
> all.decide <-
decideTests(ebfit.all.contrasts,adjust.method="BH",p.value=0.05)
> summary(all.decide)
D1R D1NR D2R D2NR
-1 1 0 5 2
0 29470 29474 29423 29471
1 1 0 56 2
#######################################
DE analysis without "arrayWeights"
#######################################
> fit.all <-lmFit(DiffEx_all,DiffEx.design)
> ebfit.all <- eBayes(fit.all)
> all_contrasts <- makeContrasts(D1R= D1_R.-Contr,D1NR=D1_NR-Contr,D2R
=D2_R-Contr,D2NR=D2_NR-Contr,levels=DiffEx.design)
> ebfit.all.contrasts <- contrasts.fit(ebfit.all, all_contrasts)
> ebfit.all.contrasts <- eBayes(ebfit.all.contrasts)
> all.decide <-
decideTests(ebfit.all.contrasts,adjust.method="BH",p.value=0.05)
> all.decide <- decideTests(ebfit.all.contrasts,p.value=0.05)
> summary(all.decide)
D1R D1NR D2R D2NR
-1 1 0 3 2
0 29467 29473 29443 29471
1 3 0 48 1
#############################################
-- output of sessionInfo():
aaa
--
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