[BioC] Limma Design

[claudio.is at libero.it]

Dear BioC,

I am tring to use Limma package in order to analyze miRNA expression. I would like to identify differentially expressed miRNA; my experimental design encompasses dye swap, and different technical replicates:

REF expA1
REF expB1
REF expC1
the corensponing dye-swap
expA1 REF
expB1 REF
expC1 REF

REF expA2
REF expB2
REF expC2
the corensponing dye-swap
expA2 REF
expB2 REF
expC2 REF

REF expA3
REF expB3
REF expC3
the corensponing dye-swap
expA3 REF
expB3 REF
expC3 REF

I how can I set the design matrix for linear model in order to identify differentially regulated genes in respect to the comaparison between A vs B, A vs C and B vs C. I tried with
fit <- lmFit(MA, design=c(1,2,3,-1,-2,-3,1,2,3,-1,-2,-3,1,2,3,-1,-2,-3))

but I get results that are too much different for t-test among conditions, so I think it is wrong.

thank you

Claudio




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