Question: Affymetrix internal control up-regulated, is anything wrong?

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Guest User •

**12k**wrote:
I am a very beginner with array data analysis.
I have 3 groups CTR and TREATMENT1 and TREATMENT2. I used a very
simple design to perform the 3 comparisons, but I found that 2 out 3
Affymetric probesets for actin beta resulted up-regulated in the CTR
condition. All the other probsets for actin beta don't significantly
change.
Is that normal? could it be a sign of something wrong either during
the hybridization or during the analysis?
Thanks
-- output of sessionInfo():
eset = exprs(expr)[, c(1:18)]
designM = model.matrix(~ 0 + factor(c("C", "C", "C", "C", "C", "C",
"T1", "T1", "T1", "T1", "T1", "T1", "T2", "T2", "T2", "T2", "T2",
"T2"), levels = c("C", "T1", "T2")))
colnames(designM) = c("C", "T1", "T2")
fit <- lmFit(eset, designM)
contrast.matrix <- makeContrasts(C-T1, C-T2, T1-T2, levels = designM)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
--
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modified 6.8 years ago
by
James W. MacDonald ♦

**48k**• written 6.8 years ago by Guest User •**12k**