[BioC] Post-hoc correction fro htQPCR

[alessandro.guffanti at genomnia.com]

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)



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