Post-hoc correction fro htQPCR
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 9.6 years ago
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) > > > > ----------------------------------------------------------- > Il Contenuto del presente messaggio potrebbe contenere informazioni > confidenziali a favore dei > soli destinatari del messaggio stesso. Qualora riceviate per errore questo > messaggio siete pregati > di cancellarlo dalla memoria del computer e di contattare i numeri sopra > indicati. Ogni utilizzo o > ritrasmissione dei contenuti del messaggio da parte di soggetti diversi > dai destinatari ? da > considerarsi vietato ed abusivo. > > The information transmitted is intended only for the p...{{dropped:13}}
HTqPCR HTqPCR • 1.0k views
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@alessandroguffantigenomniacom-4436
Last seen 9.6 years ago
Thanks a lot Heidi. There was a bug, apparently, in the previous version of R x64 which prevented me to see some of the help files but not all of them (I swear!!). Inow tried a ?ttestCtData on R x64 2.12.1 and it worked fine Yes, you have in your mailbox two mails for me which I summarize here (sme of the questions having been answered or solved). The word in attach refers to the second question posted below Keep in touch, Alessandro --- Hi Heidi ! My name is Alessandro and i am a bioinformatician in a small genome services company in Italy. We tested HTqpCR in a set of 20 ABI 7900 qPCR experiments with interesting results (hence thank you so much for these libraries!!) but I do have a couple of questions for you: - the library needs in input SDS output files, which contain the Ct values called by the SDS software, Now, it is possible to get these values automatically from SDS or manually, trying to consider global baseline and threshold settings for all the experiments. In your experience, which is the most common strategy for such kind of experiments which I would define medium scale ? --- Dear Heidi, in addition to my previous questions, and sorry for bothering you again: from the attached documents you will see that one of the samples (04.5321.T0) apparently has a very bad Ct values range. Still, I did get a look by eye and I do not see anything too peculiar on this sample, neither I saw it with another sample. I know it is a rather generic question, but how do you think this situation could be generated ? too many Ct values near 35-40 ? On 1/14/2011 5:31 PM, Heidi Dvinge wrote: > 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: > -- 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) ----------------------------------------------------------- Il Contenuto del presente messaggio potrebbe contenere informazioni confidenziali a favore dei soli destinatari del messaggio stesso. Qualora riceviate per errore questo messaggio siete pregati di cancellarlo dalla memoria del computer e di contattare i numeri sopra indicati. Ogni utilizzo o ritrasmissione dei contenuti del messaggio da parte di soggetti diversi dai destinatari ? da considerarsi vietato ed abusivo. The information transmitted is intended only for the person or entity to which it is addressed and contains confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. -----------------------------------------------------------

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