[BioC] Post-hoc correction fro htQPCR

[Heidi Dvinge]

Dear Alessandro,

> Dear Heidi, hope your 2011 will be rich of positive novelties!
>
> I have a rather important HTqPCR question for you, which I can not
> answer by myself
> since the help for these statistical test function seemingly do not work
>
> Could you detail me which kind of adjustment for multiple tests are you
> performing here ?
> Bonferroni ?
>
For ttestCtData the default is set to p.adjust="BH", as specified in the
help file, aka Benjamini & Hochberg. Internally, the ttestCtData calls the
function p.adjust to correct the p-values. ?p.adjust will give you a lot
more information about the available methods, including literature
references. If you are specifically interested in Bonferroni, you can say:

> data(qPCRpros)
> diff.exp <- ttestCtData(qPCRpros[,1:4], groups=factor(c("A", "B", "B",
"A")), calibrator="B", p.adjust="bonferroni")
> # For a comparison with the default:
> diff.exp2 <- ttestCtData(qPCRpros[,1:4], groups=factor(c("A", "B", "B",
"A")), calibrator="B")
> plot(diff.exp$adj.p.value, diff.exp2$adj.p.value, xlab="Bonferroni",
ylab="BH")

For limmaCtData, the results are passed to the topTable function from the
limma package, which again internally uses the p.adjust function. It's
therefore possible to change the p-value adjustment using the parameter
adjust.method, as specified in ?topTable. Per default that is also set to
"BH".

HTH
\Heidi

P.S. I have a nagging suspicion that I have another email with questions
from you that just drowned in my inbox over the holiday. Sorry 'bout that,
will try to dig them out now.

> Keep in touch,
>
> Alessandro G
>
>>  qDE.ttest <- ttestCtData(d.norm[,1:18],groups=files$Treatment[1:18])
>
>>  head(qDE.ttest)
>
> genes feature.post.testp.value adj.p.valueddCtFC meanCalibrator
>
> 130hsa-miR-130b#-002114Target 6.692585 5.285852e-06 0.002779618
> -2.226944 4.6814148.330278
>
>
>
>
>
> --
>
> Alessandro Guffanti - Bioinformatics, Genomnia srl
>   Via Nerviano, 31 - 20020 Lainate, Milano, Italy
>      Ph: +39-0293305.702 Fax: +39-0293305.777
>              http://www.genomnia.com
> "Keep moving forward!" (Wilbur, Meet The Robinsons)
>
>
>
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